Mercurial > repos > galaxyp > openms_siriusadapter

--- a/SiriusAdapter.xml	Mon Dec 14 16:53:26 2020 +0000
+++ b/SiriusAdapter.xml	Thu Dec 01 19:16:56 2022 +0000
@@ -1,13 +1,11 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
   <macros>
     <token name="@EXECUTABLE@">SiriusAdapter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,6 +14,10 @@
 #import re

 ## Preprocessing
+#if $sirius_executable:
+  mkdir sirius_executable &&
+  ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' &&
+#end if
 mkdir in &&
 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $in_featureinfo:
@@ -38,6 +40,10 @@
 @EXECUTABLE@ -write_ctd ./ &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
+#if $sirius_executable:
+  -sirius_executable
+  'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)'
+#end if
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 #if $in_featureinfo:
@@ -75,81 +81,84 @@
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
-    <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
-    <section name="preprocessing" title="Preprocessing" help="" expanded="false">
-      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Features have to have at least x MassTraces" help="To use this parameter feature_only is neccessary"/>
-      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="0.005" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
-      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help="">
-        <option value="Da" selected="true">Da</option>
-        <option value="ppm">ppm</option>
-        <expand macro="list_string_san"/>
+    <param argument="-sirius_executable" type="data" format="txt" optional="true" value="sirius" label="The Sirius executable" help="Provide a full or relative path, or make sure it can be found in your PATH environment select txt data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
+    <param argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
+    <param argument="-out_project_space" type="text" optional="true" value="" label="Output directory for SIRIUS project space" help="">
+      <expand macro="list_string_san" name="out_project_space"/>
+    </param>
+    <section name="preprocessing" title="" help="" expanded="false">
+      <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
+      <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
+      <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance" help="">
+        <option value="Da">Da</option>
+        <option value="ppm" selected="true">ppm</option>
+        <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
       </param>
-      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="integer" optional="true" value="5" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
+      <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
       <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" optional="true" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
       <param name="feature_only" argument="-preprocessing:feature_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature" help=""/>
       <param name="no_masstrace_info_isotope_pattern" argument="-preprocessing:no_masstrace_info_isotope_pattern" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead" help=""/>
     </section>
-    <section name="sirius" title="Parameters for SIRIUS and CSI:FingerID" help="" expanded="false">
-      <param name="profile" argument="-sirius:profile" display="radio" type="select" optional="false" label="Specify the used analysis profile" help="">
+    <section name="project" title="" help="" expanded="false">
+      <param name="processors" argument="-project:processors" type="integer" optional="true" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
+      <param name="ignore_formula" argument="-project:ignore_formula" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore given molecular formula in internal .ms format, while processing" help=""/>
+      <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
+    </section>
+    <section name="sirius" title="" help="" expanded="false">
+      <param name="ppm_max" argument="-sirius:ppm_max" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
+      <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
+      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
+      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
+      <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
+      <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help="">
+        <option value="default">default</option>
         <option value="qtof" selected="true">qtof</option>
         <option value="orbitrap">orbitrap</option>
         <option value="fticr">fticr</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="profile"/>
+      </param>
+      <param name="formula" argument="-sirius:formula" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
+        <expand macro="list_string_san" name="formula"/>
+      </param>
+      <param name="ions_enforced" argument="-sirius:ions_enforced" type="text" optional="true" value="" label="The iontype/adduct of the MS/MS data" help="Example: [M+H]+, . [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a . comma separated list of adducts">
+        <expand macro="list_string_san" name="ions_enforced"/>
+      </param>
+      <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of formula candidates in the SIRIUS output" help=""/>
+      <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" optional="true" value="-1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results. -1 omits parameter in Sirius"/>
+      <param name="elements_considered" argument="-sirius:elements_considered" type="text" optional="true" value="" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
+        <expand macro="list_string_san" name="elements_considered"/>
       </param>
-      <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of candidates in the SIRIUS output" help=""/>
-      <param name="database" argument="-sirius:database" type="select" optional="false" label="search formulas in given database" help="">
-        <option value="all" selected="true">all</option>
-        <option value="chebi">chebi</option>
-        <option value="custom">custom</option>
-        <option value="kegg">kegg</option>
-        <option value="bio">bio</option>
-        <option value="natural products">natural products</option>
-        <option value="pubmed">pubmed</option>
-        <option value="hmdb">hmdb</option>
-        <option value="biocyc">biocyc</option>
-        <option value="hsdb">hsdb</option>
-        <option value="knapsack">knapsack</option>
-        <option value="biological">biological</option>
-        <option value="zinc bio">zinc bio</option>
-        <option value="gnps">gnps</option>
-        <option value="pubchem">pubchem</option>
-        <option value="mesh">mesh</option>
-        <option value="maconda">maconda</option>
-        <expand macro="list_string_san"/>
+      <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" optional="true" value="" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound. Default is CHNOP">
+        <expand macro="list_string_san" name="elements_enforced"/>
+      </param>
+      <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/>
+      <param name="no_isotope_filter" argument="-sirius:no_isotope_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable molecular formula filte" help="When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score"/>
+      <param name="ions_considered" argument="-sirius:ions_considered" type="text" optional="true" value="" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
+        <expand macro="list_string_san" name="ions_considered"/>
       </param>
-      <param name="noise" argument="-sirius:noise" type="integer" optional="true" min="0" value="0" label="median intensity of noise peaks" help=""/>
-      <param name="ppm_max" argument="-sirius:ppm_max" type="integer" optional="true" value="10" label="allowed ppm for decomposing masses" help=""/>
-      <param name="isotope" argument="-sirius:isotope" display="radio" type="select" optional="false" label="how to handle isotope pattern data" help="Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring. Use 'omit' to ignore isotope pattern">
-        <option value="score">score</option>
-        <option value="filter">filter</option>
-        <option value="both" selected="true">both</option>
-        <option value="omit">omit</option>
-        <expand macro="list_string_san"/>
+      <param name="db" argument="-sirius:db" type="text" optional="true" value="" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+        <expand macro="list_string_san" name="db"/>
       </param>
-      <param name="elements" argument="-sirius:elements" type="text" optional="true" value="CHNOP[5]S[8]Cl[1]" label="The allowed elements" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1]">
-        <expand macro="list_string_san"/>
+    </section>
+    <section name="fingerid" title="" help="" expanded="false">
+      <param name="candidates" argument="-fingerid:candidates" type="integer" optional="true" min="1" value="10" label="Number of molecular structure candidates in the output" help=""/>
+      <param name="db" argument="-fingerid:db" type="text" optional="true" value="BIO" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
+        <expand macro="list_string_san" name="db"/>
       </param>
-      <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/>
-      <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/>
-      <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/>
-      <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
-      <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/>
-      <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/>
-      <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="converter_mode" argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to only convert the input mzML and featureXML to an .ms file" help="Without further SIRIUS processing"/>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <param argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to convert the input mzML and featureXML to a .ms file" help="Without further SIRIUS processing"/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
-      <option value="out_sirius_FLAG">out_sirius (MzTab Output file for SiriusAdapter results)</option>
+      <option value="out_sirius_FLAG">out_sirius (MzTab output file for SIRIUS results)</option>
       <option value="out_fingerid_FLAG">out_fingerid (MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formula)</option>
       <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
@@ -172,13 +181,496 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SiriusAdapter"/>
-    <expand macro="manutest_SiriusAdapter"/>
+  <tests><!-- TOPP_SiriusAdapter_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="SiriusAdapter_1_input.mzML"/>
+      <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="1"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="false"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value="all"/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="SiriusAdapter_2_input.mzML"/>
+      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
+      <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="3"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="true"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value="all"/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="SiriusAdapter_3_input.mzML"/>
+      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
+      <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="3"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="false"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value="all"/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_5 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="true"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="SiriusAdapter_3_input.mzML"/>
+      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
+      <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="1"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="false"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value=""/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_6 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="true"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="SiriusAdapter_4_input.mzML"/>
+      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
+      <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="1"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="false"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value=""/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_8 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
+      <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
+      <output name="out_sirius" file="SiriusAdapter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="1"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="true"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value="all"/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_9 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
+      <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
+      <output name="out_sirius" file="SiriusAdapter_9_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="1"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="false"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value="all"/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_7 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="converter_mode" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="SiriusAdapter_4_input.mzML"/>
+      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
+      <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="1"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="true"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value="all"/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_SiriusAdapter_4 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="converter_mode" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="SiriusAdapter_2_input.mzML"/>
+      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
+      <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <param name="out_project_space" value=""/>
+      <section name="preprocessing">
+        <param name="filter_by_num_masstraces" value="1"/>
+        <param name="precursor_mz_tolerance" value="10.0"/>
+        <param name="precursor_mz_tolerance_unit" value="ppm"/>
+        <param name="precursor_rt_tolerance" value="5.0"/>
+        <param name="isotope_pattern_iterations" value="3"/>
+        <param name="feature_only" value="false"/>
+        <param name="no_masstrace_info_isotope_pattern" value="false"/>
+      </section>
+      <section name="project">
+        <param name="processors" value="1"/>
+        <param name="ignore_formula" value="false"/>
+        <param name="q" value="false"/>
+      </section>
+      <section name="sirius">
+        <param name="ppm_max" value="10.0"/>
+        <param name="ppm_max_ms2" value="10.0"/>
+        <param name="tree_timeout" value="0"/>
+        <param name="compound_timeout" value="100"/>
+        <param name="no_recalibration" value="false"/>
+        <param name="profile" value="qtof"/>
+        <param name="formula" value=""/>
+        <param name="ions_enforced" value=""/>
+        <param name="candidates" value="5"/>
+        <param name="candidates_per_ion" value="-1"/>
+        <param name="elements_considered" value=""/>
+        <param name="elements_enforced" value=""/>
+        <param name="no_isotope_score" value="false"/>
+        <param name="no_isotope_filter" value="false"/>
+        <param name="ions_considered" value=""/>
+        <param name="db" value="ALL"/>
+      </section>
+      <section name="fingerid">
+        <param name="candidates" value="10"/>
+        <param name="db" value="BIO"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry


-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SiriusAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SiriusAdapter.html]]></help>
   <expand macro="references"/>
 </tool>
--- a/fill_ctd.py	Mon Dec 14 16:53:26 2020 +0000
+++ b/fill_ctd.py	Thu Dec 01 19:16:56 2022 +0000
@@ -32,7 +32,7 @@
     for k, v in e.items():
         if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
             mergeDicts(d[k], e[k])
-        elif k not in d and not isinstance(e[k], collections.abc.Mapping):
+        elif k not in d:
             d[k] = e[k]
         else:
             sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
@@ -135,9 +135,10 @@
 # insert the hc_args into the args
 mergeDicts(args, hc_args)

-if "adv_opts_cond" in args:
-    args.update(args["adv_opts_cond"])
-    del args["adv_opts_cond"]
+# put the contents of the advanced options section into the main dict
+if "adv_opts" in args:
+    args.update(args["adv_opts"])
+    del args["adv_opts"]

 # IDMapper has in and spectra:in params, in is used in out as format_source",
 # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fill_ctd_clargs.py	Thu Dec 01 19:16:56 2022 +0000
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+
+import operator
+from argparse import ArgumentParser
+from functools import reduce  # forward compatibility for Python 3
+from io import StringIO
+
+from CTDopts.CTDopts import (
+    _Null,
+    CTDModel,
+    ModelTypeError,
+    Parameters
+)
+
+
+def getFromDict(dataDict, mapList):
+    return reduce(operator.getitem, mapList, dataDict)
+
+
+def setInDict(dataDict, mapList, value):
+    getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
+
+
+if __name__ == "__main__":
+    # note add_help=False since otherwise arguments starting with -h will
+    # trigger an error (despite allow_abbreviate)
+    parser = ArgumentParser(prog="fill_ctd_clargs",
+                            description="fill command line arguments"
+                            "into a CTD file and write the CTD file to stdout",
+                            add_help=False, allow_abbrev=False)
+    parser.add_argument("--ini_file", dest="ini_file", help="input ini file",
+                        metavar='INI', default=None, required=True)
+    parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file"
+                        "if given then optional parameters from the ini file"
+                        "will be filled with the defaults from this CTD file",
+                        metavar='CTD', default=None, required=False)
+    args, cliargs = parser.parse_known_args()
+
+    # load CTDModel
+    ini_model = None
+    try:
+        ini_model = CTDModel(from_file=args.ini_file)
+    except ModelTypeError:
+        pass
+    try:
+        ini_model = Parameters(from_file=args.ini_file)
+    except ModelTypeError:
+        pass
+    assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file)
+
+    # get a dictionary of the ctd arguments where the values of the parameters
+    # given on the command line are overwritten
+    ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True)
+
+    if args.ctd_file:
+        ctd_model = CTDModel(from_file=args.ctd_file)
+        ctd_values = ctd_model.get_defaults()
+        for param in ini_model.get_parameters():
+            if not param.required and (param.default is None or type(param.default) is _Null):
+                lineage = param.get_lineage(name_only=True)
+                try:
+                    default = getFromDict(ctd_values, lineage)
+                except KeyError:
+                    continue
+                setInDict(ini_values, lineage, default)
+
+    # write the ctd with the values taken from the dictionary
+    out = StringIO()
+    ctd_tree = ini_model.write_ctd(out, ini_values)
+    print(out.getvalue())
--- a/generate-foo.sh	Mon Dec 14 16:53:26 2020 +0000
+++ b/generate-foo.sh	Thu Dec 01 19:16:56 2022 +0000
@@ -8,17 +8,15 @@

     # get the tests from the CMakeLists.txt
     # 1st remove some tests
-    # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399
+    # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
     # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
     # - several tools with duplicated input (leads to conflict when linking)
-    # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
     # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
     # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
     # - some input files are originally in a subdir (degenerated cases/), but not in test-data
-    # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
     # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
-    # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002
-    # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
+    # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869
     CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
         sed 's@${DATA_DIR_SHARE}/@@g' |
         grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
@@ -26,19 +24,9 @@
         grep -v "MaRaClusterAdapter.*-consensus_out"|
         grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
         sed 's@degenerate_cases/@@g' |
-        grep -v 'TOPP_SeedListGenerator_3"' |
         egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
-	egrep -v '"TOPP_FeatureFinderIdentification_4"' |
-	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/')
-
-
-#         grep -v 'FileFilter.*-spectra:select_polarity ""' |
-#         grep -v 'MassTraceExtractor_2.ini ' |
-#         grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
-#         grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
-#         grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
-#         grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
-#         grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
+        sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
+        grep -v '"TOPP_SiriusAdapter_10"')

     # 1st part is a dirty hack to join lines containing a single function call, e.g.
     # addtest(....
@@ -50,6 +38,7 @@
         # >&2 echo $line
         test_id=$(echo "$line" | cut -d" " -f 1)
         tool_id=$(echo "$line" | cut -d" " -f 2)
+        # >&2 echo "test_id $test_id"
         if [[ $test_id =~ _out_?[0-9]? ]]; then
             >&2 echo "    skip $test_id $line"
             continue
@@ -67,7 +56,7 @@
         tes="  <test>\n"
         line=$(fix_tmp_files "$line")
         line=$(unique_files "$line")
-        # >&2 echo $line
+        # >&2 echo LINE $line
         #if there is an ini file then we use this to generate the test
         #otherwise the ctd file is used
         #other command line parameters are inserted later into this xml
@@ -77,19 +66,23 @@
         else
             ini="ctd/$tool_id.ctd"
         fi
+        # >&2 echo "========================================================"
+        # >&2 echo "USING ini $ini"
         cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')

         ctdtmp=$(mktemp)
-        #echo python3 fill_ctd_clargs.py --ctd $ini $cli
         # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
-        # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
-        eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp"
-        # echo $ctdtmp
+        # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli"
+        eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp"
+        # >&2 echo $ctdtmp
         # >&2 cat $ctdtmp
         testtmp=$(mktemp)
-        python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null
+        # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7"
+        CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null
+        echo "<!-- $test_id -->"
         cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
-        rm $ctdtmp $testtmp
+
+        rm "$ctdtmp" "$testtmp"

         #> /dev/null

@@ -130,23 +123,23 @@
 #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
 #this function replaces the tmp file by the expected file.
 function fix_tmp_files {
-#    >&2 echo "FIX $line"
+    # >&2 echo "FIX $line"
     ret=""
     for a in $@; do
-        if [[ ! $a =~ .tmp$ ]]; then
+        # >&2 echo "    a "$a
+        if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then
             ret="$ret $a"
             continue
         fi
-#        >&2 echo "    a "$a
-        g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
-#        >&2 echo "    g "$g
-        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g)
+        diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
+        # >&2 echo "    diff_line "$diff_line
+        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line)
         # >&2 echo "    in1 "$in1
         if [[  "$a" != "$in1" ]]; then
             ret="$ret $a"
             continue
         fi
-        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g)
+        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line)
         in2=$(basename $in2 | sed 's/)$//')
         # >&2 echo "    in2 "$in2
         if [[ -f "test-data/$in2" ]]; then
@@ -176,11 +169,11 @@
         fi
         ln -f -s $in1 test-data/$in2
     done
-    for i in test-data/*.tmp
-    do
+
+    find test-data/ -name "*.tmp" -print0 |
+    while IFS= read -r -d '' i; do
         if [ ! -e test-data/$(basename $i .tmp) ]; then
             ln -s $(basename $i) test-data/$(basename $i .tmp)
-            #ln -s $(basename $i) test-data/$(basename $i .tmp)
         else
             ln -fs $(basename $i) test-data/$(basename $i .tmp)
         fi
@@ -194,14 +187,14 @@
 #     id=$1
 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"

-# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
     cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' |
         sed 's/degenerate_cases\///' |
         egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" |
         grep add_test |
         egrep "TOPP|UTILS" |
         sed 's@${DATA_DIR_SHARE}/@@g;'|
-        sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'|
+        sed 's@${TMP_RIP_PATH}@./@g'|
         sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'|
 	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
     while read line
--- a/macros.xml	Mon Dec 14 16:53:26 2020 +0000
+++ b/macros.xml	Thu Dec 01 19:16:56 2022 +0000
@@ -3,14 +3,15 @@
      You can edit this file to add your own macros, if you so desire, or you can
      add additional macro files using the m/macros parameter -->
 <macros>
-  <token name="@TOOL_VERSION@">2.6</token>
-  <token name="@GALAXY_VERSION@">0</token>
+  <token name="@TOOL_VERSION@">2.8</token>
+  <token name="@VERSION_SUFFIX@">0</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
       <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
-      <!-- makeblastdb for OMSSAAdapter -->
-      <requirement type="package" version="2.9.0">blast</requirement>
+      <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter -->
+      <requirement type="package" version="2.1.9">omssa</requirement>
+      <requirement type="package" version="2.13.0">blast</requirement>
       <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
       <!-- for realpath (used e.g. in LuciphorAdapter) -->
 	  <!--<requirement type="package" version="8.25">coreutils</requirement>-->
@@ -33,23 +34,15 @@
     </citations>
   </xml>
   <xml name="adv_opts_macro">
-    <conditional name="adv_opts_cond">
-      <param name="adv_opts_selector" type="select" label="Advanced Options">
-        <option value="basic" selected="True">Hide Advanced Options</option>
-        <option value="advanced">Show Advanced Options</option>
-      </param>
-      <when value="basic"/>
-      <when value="advanced">
-        <yield/>
-      </when>
-    </conditional>
+    <section name="adv_opts" title="Advanced Options" expanded="false">
+      <yield/>
+    </section>
   </xml>

   <!-- sanitizers and validators -->
-  <xml name="list_string_val">
-    <validator type="regex" message="parameter must not start with $">^[^$]</validator>
-
-    <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
+  <xml name="list_string_val" token_name="">
+    <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator>
+    <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
   </xml>
   <xml name="list_string_san">
     <sanitizer>
@@ -65,8 +58,8 @@
       </valid>
     </sanitizer>
   </xml>
-  <xml name="list_float_valsan">
-    <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator>
+  <xml name="list_float_valsan" token_name="">
+    <validator type="regex" message="parameter @NAME@: a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator>
     <yield/>
     <sanitizer>
       <valid initial="string.digits">
@@ -79,8 +72,8 @@
       </valid>
     </sanitizer>
   </xml>
-  <xml name="list_integer_valsan">
-    <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
+  <xml name="list_integer_valsan" token_name="">
+    <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
     <yield/>
     <sanitizer>
       <valid initial="string.digits">
@@ -120,11 +113,11 @@
   </token>

 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
-    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
+    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
     #return m[o]
 #end def
 #def gxy2omsext(g)
-    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
+    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
     #return m[g]
 #end def
 ]]></token></macros>
--- a/macros_autotest.xml	Mon Dec 14 16:53:26 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27189 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<macros>
-  <xml name="autotest_AccurateMassSearch">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
-      <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
-      <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
-      <section name="db">
-        <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>
-        <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/>
-      </section>
-      <section name="algorithm">
-        <param name="mass_error_value" value="5.0"/>
-        <param name="mass_error_unit" value="ppm"/>
-        <param name="ionization_mode" value="positive"/>
-        <param name="isotopic_similarity" value="false"/>
-        <param name="use_feature_adducts" value="false"/>
-        <param name="keep_unidentified_masses" value="false"/>
-        <section name="mzTab">
-          <param name="exportIsotopeIntensities" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
-      <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
-      <section name="db">
-        <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
-        <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
-      </section>
-      <section name="algorithm">
-        <param name="mass_error_value" value="5.0"/>
-        <param name="mass_error_unit" value="ppm"/>
-        <param name="ionization_mode" value="positive"/>
-        <param name="isotopic_similarity" value="false"/>
-        <param name="use_feature_adducts" value="false"/>
-        <param name="keep_unidentified_masses" value="false"/>
-        <section name="mzTab">
-          <param name="exportIsotopeIntensities" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
-      <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
-      <section name="db">
-        <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
-        <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
-      </section>
-      <section name="algorithm">
-        <param name="mass_error_value" value="5.0"/>
-        <param name="mass_error_unit" value="ppm"/>
-        <param name="ionization_mode" value="positive"/>
-        <param name="isotopic_similarity" value="false"/>
-        <param name="use_feature_adducts" value="false"/>
-        <param name="keep_unidentified_masses" value="false"/>
-        <section name="mzTab">
-          <param name="exportIsotopeIntensities" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_AssayGeneratorMetabo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="consensus_spectrum"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="consensus_spectrum"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="consensus_spectrum"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="true"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="true"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_BaselineFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="BaselineFilter_input.mzML"/>
-      <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="struc_elem_length" value="1.5"/>
-      <param name="struc_elem_unit" value="Thomson"/>
-      <param name="method" value="tophat"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ClusterMassTracesByPrecursor">
-</xml>
-  <xml name="autotest_ClusterMassTraces">
-</xml>
-  <xml name="autotest_CometAdapter">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:5000"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="1000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="5"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_mass_tolerance" value="3.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.50025"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.25"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep any known"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value=""/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:5000"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="1000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="5"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CometAdapter_2_prepared.mzML"/>
-      <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="CometAdapter_2_in.fasta"/>
-      <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_mass_tolerance" value="3.0"/>
-      <param name="precursor_error_units" value="Da"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.50025"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.25"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep any known"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value=""/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:5000"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="20000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="3"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CometAdapter_3.mzML"/>
-      <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="CometAdapter_3.fasta"/>
-      <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.01"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.0"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="3"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep known search unknown"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
-      <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:1200"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="20000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="3"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
-      <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.01"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.0"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="3"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep known search unknown"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
-      <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CompNovoCID">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CompNovoCID_1_input.mzML"/>
-      <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="algorithm">
-        <param name="max_number_aa_per_decomp" value="4"/>
-        <param name="tryptic_only" value="true"/>
-        <param name="precursor_mass_tolerance" value="0.3"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="max_number_pivot" value="9"/>
-        <param name="max_subscore_number" value="40"/>
-        <param name="decomp_weights_precision" value="0.01"/>
-        <param name="double_charged_iso_threshold" value="0.6"/>
-        <param name="max_mz" value="2000.0"/>
-        <param name="min_mz" value="200.0"/>
-        <param name="max_isotope_to_score" value="3"/>
-        <param name="max_decomp_weight" value="450.0"/>
-        <param name="max_isotope" value="3"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="estimate_precursor_mz" value="true"/>
-        <param name="number_of_prescoring_hits" value="250"/>
-        <param name="fixed_modifications" value=""/>
-        <param name="variable_modifications" value=""/>
-        <param name="residue_set" value="Natural19WithoutI"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CompNovo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CompNovo_1_input.mzML"/>
-      <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="algorithm">
-        <param name="max_number_aa_per_decomp" value="4"/>
-        <param name="tryptic_only" value="true"/>
-        <param name="precursor_mass_tolerance" value="0.3"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="max_number_pivot" value="9"/>
-        <param name="max_subscore_number" value="40"/>
-        <param name="decomp_weights_precision" value="0.01"/>
-        <param name="double_charged_iso_threshold" value="0.6"/>
-        <param name="max_mz" value="2000.0"/>
-        <param name="min_mz" value="200.0"/>
-        <param name="max_isotope_to_score" value="3"/>
-        <param name="max_decomp_weight" value="450.0"/>
-        <param name="max_isotope" value="3"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="estimate_precursor_mz" value="true"/>
-        <param name="number_of_prescoring_hits" value="250"/>
-        <param name="fixed_modifications" value=""/>
-        <param name="variable_modifications" value=""/>
-        <param name="residue_set" value="Natural19WithoutI"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ConsensusID">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="PEPMatrix"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="PAM30MS"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_2_input.featureXML"/>
-      <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="average"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_3_input.consensusXML"/>
-      <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="PEPMatrix"/>
-      <section name="filter">
-        <param name="considered_hits" value="6"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="PEPIons"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.5"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_6_input.idXML"/>
-      <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="true"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="true"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_8_input.idXML"/>
-      <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="true"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="true"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ConsensusMapNormalizer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="accession_filter" value=""/>
-        <param name="description_filter" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
-      <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="algorithm_type" value="robust_regression"/>
-      <param name="ratio_threshold" value="0.67"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CruxAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="custom_enzyme" value=""/>
-        <param name="decoy_prefix" value="decoy_"/>
-        <param name="deisotope" value="false"/>
-        <param name="report_decoys" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="extra_index_args" value=""/>
-      <param name="extra_search_args" value=""/>
-      <param name="extra_percolator_args" value=""/>
-      <param name="precursor_mass_tolerance" value="10.0"/>
-      <param name="precursor_mass_units" value="ppm"/>
-      <param name="fragment_bin_offset" value="0.0"/>
-      <param name="fragment_bin_width" value="0.02"/>
-      <param name="isotope_error" value=""/>
-      <param name="run_percolator" value="false"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="digestion" value="full-digest"/>
-      <param name="allowed_missed_cleavages" value="0"/>
-      <param name="decoy_format" value="peptide-reverse"/>
-      <param name="keep_terminal_aminos" value="NC"/>
-      <param name="cterm_modifications" value=""/>
-      <param name="nterm_modifications" value=""/>
-      <param name="modifications" value=""/>
-      <param name="test_fdr" value="0.01"/>
-      <param name="train_fdr" value="0.01"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CVInspector">
-</xml>
-  <xml name="autotest_DatabaseFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_1.fasta"/>
-      <param name="id" value="DatabaseFilter_1.idXML"/>
-      <param name="method" value="whitelist"/>
-      <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_1.fasta"/>
-      <param name="id" value="DatabaseFilter_1.idXML"/>
-      <param name="method" value="blacklist"/>
-      <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_3.fasta"/>
-      <param name="id" value="DatabaseFilter_3.mzid"/>
-      <param name="method" value="whitelist"/>
-      <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_3.fasta"/>
-      <param name="id" value="DatabaseFilter_3.mzid"/>
-      <param name="method" value="blacklist"/>
-      <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_DatabaseSuitability">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
-      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
-      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
-      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="algorithm">
-        <param name="no_rerank" value="false"/>
-        <param name="reranking_cutoff_percentile" value="0.01"/>
-        <param name="FDR" value="0.8"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
-      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
-      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
-      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="algorithm">
-        <param name="no_rerank" value="false"/>
-        <param name="reranking_cutoff_percentile" value="0.9"/>
-        <param name="FDR" value="1.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
-      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
-      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
-      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="algorithm">
-        <param name="no_rerank" value="true"/>
-        <param name="reranking_cutoff_percentile" value="0.01"/>
-        <param name="FDR" value="0.9"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_Decharger">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Decharger_input.featureXML"/>
-      <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <section name="FeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="10"/>
-          <param name="charge_span_max" value="4"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.1"/>
-          <param name="potential_adducts" value="&quot;H:+:0.7&quot; &quot;Na:+:0.1&quot; &quot;(2)H4H-4:0:0.1:-2:heavy&quot;"/>
-          <param name="max_neutrals" value="0"/>
-          <param name="max_minority_bound" value="2"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_DecoyDatabase">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_1.fasta"/>
-      <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="true"/>
-      <param name="type" value="protein"/>
-      <param name="method" value="reverse"/>
-      <param name="enzyme" value="Trypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value=""/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="42"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_1.fasta"/>
-      <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="false"/>
-      <param name="type" value="protein"/>
-      <param name="method" value="shuffle"/>
-      <param name="enzyme" value="Trypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value="KRP"/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="42"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_1.fasta"/>
-      <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="false"/>
-      <param name="type" value="protein"/>
-      <param name="method" value="shuffle"/>
-      <param name="enzyme" value="Chymotrypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value="KR"/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="42"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_4.fasta"/>
-      <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="false"/>
-      <param name="type" value="RNA"/>
-      <param name="method" value="reverse"/>
-      <param name="enzyme" value="Trypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value=""/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_DeMeanderize">
-</xml>
-  <xml name="autotest_DigestorMotif">
-</xml>
-  <xml name="autotest_Digestor">
-</xml>
-  <xml name="autotest_DTAExtractor">
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DTAExtractor_1_input.mzML"/>
-      <param name="out" value="DTAExtractor"/>
-      <param name="mz" value=":"/>
-      <param name="rt" value=":61"/>
-      <param name="level" value="1,2,3"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DTAExtractor_1_input.mzML"/>
-      <param name="out" value="DTAExtractor"/>
-      <param name="mz" value=":"/>
-      <param name="rt" value=":"/>
-      <param name="level" value="1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DTAExtractor_1_input.mzML"/>
-      <param name="out" value="DTAExtractor"/>
-      <param name="mz" value=":1000"/>
-      <param name="rt" value=":"/>
-      <param name="level" value="2"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_EICExtractor">
-</xml>
-  <xml name="autotest_Epifany">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="conservative_fdr" value="true"/>
-        <param name="min_psms_extreme_probability" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idxml"/>
-      <param name="protein_fdr" value="false"/>
-      <param name="greedy_group_resolution" value="none"/>
-      <param name="max_psms_extreme_probability" value="1.0"/>
-      <section name="algorithm">
-        <param name="psm_probability_cutoff" value="0.001"/>
-        <param name="top_PSMs" value="1"/>
-        <param name="keep_best_PSM_only" value="true"/>
-        <param name="update_PSM_probabilities" value="true"/>
-        <param name="user_defined_priors" value="false"/>
-        <param name="annotate_group_probabilities" value="true"/>
-        <param name="use_ids_outside_features" value="false"/>
-        <section name="model_parameters">
-          <param name="prot_prior" value="0.7"/>
-          <param name="pep_emission" value="0.1"/>
-          <param name="pep_spurious_emission" value="0.001"/>
-          <param name="pep_prior" value="0.1"/>
-          <param name="regularize" value="false"/>
-          <param name="extended_model" value="false"/>
-        </section>
-        <section name="loopy_belief_propagation">
-          <param name="scheduling_type" value="priority"/>
-          <param name="convergence_threshold" value="1e-05"/>
-          <param name="dampening_lambda" value="0.001"/>
-          <param name="max_nr_iterations" value="2147483647"/>
-          <param name="p_norm_inference" value="1.0"/>
-        </section>
-        <section name="param_optimize">
-          <param name="aucweight" value="0.3"/>
-          <param name="conservative_fdr" value="true"/>
-          <param name="regularized_fdr" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="conservative_fdr" value="true"/>
-        <param name="min_psms_extreme_probability" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_2_input.consensusXML"/>
-      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="protein_fdr" value="false"/>
-      <param name="greedy_group_resolution" value="none"/>
-      <param name="max_psms_extreme_probability" value="1.0"/>
-      <section name="algorithm">
-        <param name="psm_probability_cutoff" value="0.001"/>
-        <param name="top_PSMs" value="1"/>
-        <param name="keep_best_PSM_only" value="true"/>
-        <param name="update_PSM_probabilities" value="true"/>
-        <param name="user_defined_priors" value="false"/>
-        <param name="annotate_group_probabilities" value="true"/>
-        <param name="use_ids_outside_features" value="false"/>
-        <section name="model_parameters">
-          <param name="prot_prior" value="0.7"/>
-          <param name="pep_emission" value="0.1"/>
-          <param name="pep_spurious_emission" value="0.001"/>
-          <param name="pep_prior" value="0.1"/>
-          <param name="regularize" value="false"/>
-          <param name="extended_model" value="false"/>
-        </section>
-        <section name="loopy_belief_propagation">
-          <param name="scheduling_type" value="priority"/>
-          <param name="convergence_threshold" value="1e-05"/>
-          <param name="dampening_lambda" value="0.001"/>
-          <param name="max_nr_iterations" value="2147483647"/>
-          <param name="p_norm_inference" value="1.0"/>
-        </section>
-        <section name="param_optimize">
-          <param name="aucweight" value="0.3"/>
-          <param name="conservative_fdr" value="true"/>
-          <param name="regularized_fdr" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="conservative_fdr" value="true"/>
-        <param name="min_psms_extreme_probability" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_2_input.consensusXML"/>
-      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="protein_fdr" value="false"/>
-      <param name="greedy_group_resolution" value="none"/>
-      <param name="max_psms_extreme_probability" value="1.0"/>
-      <section name="algorithm">
-        <param name="psm_probability_cutoff" value="0.001"/>
-        <param name="top_PSMs" value="1"/>
-        <param name="keep_best_PSM_only" value="false"/>
-        <param name="update_PSM_probabilities" value="true"/>
-        <param name="user_defined_priors" value="false"/>
-        <param name="annotate_group_probabilities" value="true"/>
-        <param name="use_ids_outside_features" value="false"/>
-        <section name="model_parameters">
-          <param name="prot_prior" value="0.7"/>
-          <param name="pep_emission" value="0.1"/>
-          <param name="pep_spurious_emission" value="0.001"/>
-          <param name="pep_prior" value="0.1"/>
-          <param name="regularize" value="false"/>
-          <param name="extended_model" value="false"/>
-        </section>
-        <section name="loopy_belief_propagation">
-          <param name="scheduling_type" value="priority"/>
-          <param name="convergence_threshold" value="1e-05"/>
-          <param name="dampening_lambda" value="0.001"/>
-          <param name="max_nr_iterations" value="2147483647"/>
-          <param name="p_norm_inference" value="1.0"/>
-        </section>
-        <section name="param_optimize">
-          <param name="aucweight" value="0.3"/>
-          <param name="conservative_fdr" value="true"/>
-          <param name="regularized_fdr" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ERPairFinder">
-</xml>
-  <xml name="autotest_ExternalCalibration">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="offset" value="-5.5"/>
-      <param name="slope" value="0.0001"/>
-      <param name="power" value="0.0"/>
-      <param name="ms_level" value="1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="offset" value="-5.5"/>
-      <param name="slope" value="0.0001"/>
-      <param name="power" value="0.0"/>
-      <param name="ms_level" value="2"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FalseDiscoveryRate">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="true"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="true"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="true"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="false"/>
-      <param name="protein" value="true"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="true"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="0.05"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="false"/>
-      <param name="protein" value="true"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="0.3"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderCentroided">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-        <param name="pseudo_rt_shift" value="500.0"/>
-      </conditional>
-      <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
-      <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="intensity">
-          <param name="bins" value="1"/>
-        </section>
-        <section name="mass_trace">
-          <param name="mz_tolerance" value="0.02"/>
-          <param name="min_spectra" value="14"/>
-          <param name="max_missing" value="1"/>
-          <param name="slope_bound" value="0.1"/>
-        </section>
-        <section name="isotopic_pattern">
-          <param name="charge_low" value="2"/>
-          <param name="charge_high" value="2"/>
-          <param name="mz_tolerance" value="0.02"/>
-          <param name="intensity_percentage" value="10.0"/>
-          <param name="intensity_percentage_optional" value="0.1"/>
-          <param name="optional_fit_improvement" value="2.0"/>
-          <param name="mass_window_width" value="100.0"/>
-          <param name="abundance_12C" value="98.93"/>
-          <param name="abundance_14N" value="99.632"/>
-        </section>
-        <section name="seed">
-          <param name="min_score" value="0.8"/>
-        </section>
-        <section name="fit">
-          <param name="max_iterations" value="500"/>
-        </section>
-        <section name="feature">
-          <param name="min_score" value="0.7"/>
-          <param name="min_isotope_fit" value="0.8"/>
-          <param name="min_trace_score" value="0.5"/>
-          <param name="min_rt_span" value="0.333"/>
-          <param name="max_rt_span" value="2.5"/>
-          <param name="rt_shape" value="symmetric"/>
-          <param name="max_intersection" value="0.35"/>
-          <param name="reported_mz" value="monoisotopic"/>
-        </section>
-        <section name="user-seed">
-          <param name="rt_tolerance" value="5.0"/>
-          <param name="mz_tolerance" value="1.1"/>
-          <param name="min_score" value="0.5"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderIdentification">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
-      <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="batch_size" value="1000"/>
-        <param name="mz_window" value="0.1"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_quantile" value="0.95"/>
-        <param name="rt_window" value="0.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="60.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-        <param name="mapping_tolerance" value="0.0"/>
-      </section>
-      <section name="svm">
-        <param name="samples" value="0"/>
-        <param name="no_selection" value="false"/>
-        <param name="kernel" value="RBF"/>
-        <param name="xval" value="5"/>
-        <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
-        <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
-        <param name="epsilon" value="0.001"/>
-        <param name="cache_size" value="100.0"/>
-        <param name="no_shrinking" value="false"/>
-        <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
-        <param name="min_prob" value="0.0"/>
-      </section>
-      <section name="model">
-        <param name="type" value="none"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
-        <param name="each_trace" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
-      <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="batch_size" value="1000"/>
-        <param name="mz_window" value="0.1"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_quantile" value="0.95"/>
-        <param name="rt_window" value="0.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="60.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-        <param name="mapping_tolerance" value="0.0"/>
-      </section>
-      <section name="svm">
-        <param name="samples" value="0"/>
-        <param name="no_selection" value="false"/>
-        <param name="kernel" value="RBF"/>
-        <param name="xval" value="5"/>
-        <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
-        <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
-        <param name="epsilon" value="0.001"/>
-        <param name="cache_size" value="100.0"/>
-        <param name="no_shrinking" value="false"/>
-        <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
-        <param name="min_prob" value="0.0"/>
-      </section>
-      <section name="model">
-        <param name="type" value="symmetric"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
-        <param name="each_trace" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderIsotopeWavelet">
-</xml>
-  <xml name="autotest_FeatureFinderMetaboIdent">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
-      <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
-      <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="mz_window" value="5.0"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_window" value="20.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="3.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-      </section>
-      <section name="model">
-        <param name="type" value="symmetric"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
-        <param name="each_trace" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderMetabo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="300.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="false"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="100.0"/>
-          <param name="chrom_peak_snr" value="0.0"/>
-          <param name="chrom_fwhm" value="100.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="5.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="median"/>
-          <param name="trace_termination_criterion" value="sample_rate"/>
-          <param name="trace_termination_outliers" value="2"/>
-          <param name="min_sample_rate" value="0.01"/>
-          <param name="min_trace_length" value="30.0"/>
-          <param name="max_trace_length" value="3000.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="false"/>
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="10.0"/>
-          <param name="max_fwhm" value="80.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="4.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="false"/>
-          <param name="isotope_filtering_model" value="none"/>
-          <param name="mz_scoring_13C" value="false"/>
-          <param name="use_smoothed_intensities" value="false"/>
-          <param name="report_convex_hulls" value="true"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="5.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="-1.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="fixed"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="none"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="true"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="5.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="-1.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="fixed"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="none"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="true"/>
-          <param name="remove_single_traces" value="true"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="max_height"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="300.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="false"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderMRM">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMRM_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="min_rt_distance" value="10.0"/>
-        <param name="min_num_peaks_per_feature" value="5"/>
-        <param name="min_signal_to_noise_ratio" value="2.0"/>
-        <param name="write_debug_files" value="false"/>
-        <param name="resample_traces" value="false"/>
-        <param name="write_debuginfo" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderMultiplex">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="90.0"/>
-        <param name="rt_band" value="10.0"/>
-        <param name="rt_min" value="5.0"/>
-        <param name="mz_tolerance" value="40.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10.0"/>
-        <param name="peptide_similarity" value="0.8"/>
-        <param name="averagine_similarity" value="0.75"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Lys8,Arg10]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="40.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[]"/>
-        <param name="charge" value="5:15"/>
-        <param name="isotopes_per_peptide" value="5:10"/>
-        <param name="rt_typical" value="45.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="200.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="RNA"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[]"/>
-        <param name="charge" value="5:15"/>
-        <param name="isotopes_per_peptide" value="5:10"/>
-        <param name="rt_typical" value="45.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="200.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="DNA"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="charge" value="1:5"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="3.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10000000.0"/>
-        <param name="peptide_similarity" value="0.95"/>
-        <param name="averagine_similarity" value="0.8"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="spectrum_type" value="profile"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="charge" value="1:5"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="3.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10000000.0"/>
-        <param name="peptide_similarity" value="0.95"/>
-        <param name="averagine_similarity" value="0.8"/>
-        <param name="averagine_similarity_scaling" value="1.0"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="spectrum_type" value="profile"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Dimethyl4]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="40.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="31.0094"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
-        <param name="charge" value="1:7"/>
-        <param name="isotopes_per_peptide" value="3:8"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="3.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10.0"/>
-        <param name="peptide_similarity" value="0.2"/>
-        <param name="averagine_similarity" value="0.25"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="4"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="true"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[0][6.03705]"/>
-        <param name="charge" value="2:8"/>
-        <param name="isotopes_per_peptide" value="3:8"/>
-        <param name="rt_typical" value="40.0"/>
-        <param name="rt_band" value="0.0"/>
-        <param name="rt_min" value="4.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="centroid"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="charge" value="1:7"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10.0"/>
-        <param name="peptide_similarity" value="0.4"/>
-        <param name="averagine_similarity" value="0.5"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="spectrum_type" value="profile"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="true"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="labels" value="[]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="1e-05"/>
-        <param name="rt_band" value="0.0"/>
-        <param name="rt_min" value="0.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.7"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderSuperHirn">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/>
-      <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="centroiding">
-          <param name="active" value="false"/>
-          <param name="window_width" value="5"/>
-          <param name="absolute_isotope_mass_precision" value="0.01"/>
-          <param name="relative_isotope_mass_precision" value="10.0"/>
-          <param name="minimal_peak_height" value="0.0"/>
-          <param name="min_ms_signal_intensity" value="50.0"/>
-        </section>
-        <section name="ms1">
-          <param name="precursor_detection_scan_levels" value="1"/>
-          <param name="max_inter_scan_distance" value="0"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="intensity_threshold" value="1000.0"/>
-          <param name="max_inter_scan_rt_distance" value="0.1"/>
-          <param name="min_nb_cluster_members" value="4"/>
-          <param name="detectable_isotope_factor" value="0.05"/>
-          <param name="intensity_cv" value="0.9"/>
-          <param name="retention_time_tolerance" value="0.5"/>
-          <param name="mz_tolerance" value="0.0"/>
-        </section>
-        <section name="ms1_feature_merger">
-          <param name="active" value="true"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="initial_apex_tr_tolerance" value="5.0"/>
-          <param name="feature_merging_tr_tolerance" value="1.0"/>
-          <param name="intensity_variation_percentage" value="25.0"/>
-          <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
-        </section>
-        <section name="ms1_feature_selection_options">
-          <param name="start_elution_window" value="0.0"/>
-          <param name="end_elution_window" value="180.0"/>
-          <param name="mz_range_min" value="0.0"/>
-          <param name="mz_range_max" value="2000.0"/>
-          <param name="chrg_range_min" value="1"/>
-          <param name="chrg_range_max" value="5"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/>
-      <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="centroiding">
-          <param name="active" value="true"/>
-          <param name="window_width" value="5"/>
-          <param name="absolute_isotope_mass_precision" value="0.01"/>
-          <param name="relative_isotope_mass_precision" value="10.0"/>
-          <param name="minimal_peak_height" value="0.0"/>
-          <param name="min_ms_signal_intensity" value="50.0"/>
-        </section>
-        <section name="ms1">
-          <param name="precursor_detection_scan_levels" value="1"/>
-          <param name="max_inter_scan_distance" value="0"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="intensity_threshold" value="1000.0"/>
-          <param name="max_inter_scan_rt_distance" value="0.1"/>
-          <param name="min_nb_cluster_members" value="4"/>
-          <param name="detectable_isotope_factor" value="0.05"/>
-          <param name="intensity_cv" value="0.9"/>
-          <param name="retention_time_tolerance" value="0.5"/>
-          <param name="mz_tolerance" value="0.0"/>
-        </section>
-        <section name="ms1_feature_merger">
-          <param name="active" value="true"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="initial_apex_tr_tolerance" value="5.0"/>
-          <param name="feature_merging_tr_tolerance" value="1.0"/>
-          <param name="intensity_variation_percentage" value="25.0"/>
-          <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
-        </section>
-        <section name="ms1_feature_selection_options">
-          <param name="start_elution_window" value="0.0"/>
-          <param name="end_elution_window" value="180.0"/>
-          <param name="mz_range_min" value="0.0"/>
-          <param name="mz_range_max" value="2000.0"/>
-          <param name="chrg_range_min" value="1"/>
-          <param name="chrg_range_max" value="5"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerLabeled">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="rt_estimate" value="false"/>
-        <param name="rt_pair_dist" value="-1.0"/>
-        <param name="rt_dev_low" value="0.4"/>
-        <param name="rt_dev_high" value="0.4"/>
-        <param name="mz_pair_dists" value="8.0"/>
-        <param name="mz_dev" value="0.1"/>
-        <param name="mrm" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="rt_estimate" value="true"/>
-        <param name="rt_pair_dist" value="-121.0382"/>
-        <param name="rt_dev_low" value="123.3965"/>
-        <param name="rt_dev_high" value="123.3965"/>
-        <param name="mz_pair_dists" value="4.0"/>
-        <param name="mz_dev" value="0.1"/>
-        <param name="mrm" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerUnlabeledKD">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="Da"/>
-        <param name="nr_partitions" value="1"/>
-        <section name="warp">
-          <param name="enabled" value="false"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="true"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="Da"/>
-        <param name="nr_partitions" value="99999"/>
-        <section name="warp">
-          <param name="enabled" value="false"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="Da"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="false"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="Identical"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="Any"/>
-          <param name="adduct_merging" value="With_unknown_adducts"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="Any"/>
-          <param name="adduct_merging" value="Identical"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerUnlabeledQT">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="true"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="99999"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="true"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="true"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerUnlabeled">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="2.0"/>
-        <param name="use_identifications" value="false"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.5"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="2.0"/>
-        <param name="use_identifications" value="false"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.5"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="1.5"/>
-        <param name="use_identifications" value="false"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="30.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="2.0"/>
-        <param name="use_identifications" value="true"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.5"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FFEval">
-</xml>
-  <xml name="autotest_FidoAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="true"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="true"/>
-      <param name="group_level" value="true"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_4_input.idXML"/>
-      <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_5_input.idXML"/>
-      <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="true"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.9"/>
-        <param name="peptide" value="0.01"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_1_input.mzData"/>
-      <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
-      <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_3_input.featureXML"/>
-      <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_4_input.mzXML"/>
-      <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_5_input.mzML"/>
-      <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_6_input.mzML"/>
-      <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_7_input.consensusXML"/>
-      <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_8_input.mzML"/>
-      <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/>
-      <param name="out_type" value="mzData"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_9_input.consensusXML"/>
-      <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_11_input.peplist"/>
-      <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
-      <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
-      <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_9_output.featureXML"/>
-      <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_17_input.consensusXML"/>
-      <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="out_type" value="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_17_input.consensusXML"/>
-      <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="out_type" value="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_20_input.featureXML"/>
-      <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_4_input.mzXML"/>
-      <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_23_input.mzML"/>
-      <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="true"/>
-        <param name="lossy_mass_accuracy" value="0.0001"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="true"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="true"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="true"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_26_output.mzXML"/>
-      <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="true"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_27_input.mzML"/>
-      <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="true"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_28_input.mzML"/>
-      <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="true"/>
-        <param name="lossy_mass_accuracy" value="1e-05"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_29_output.mzML"/>
-      <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="multiple"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_30_input.mzML"/>
-      <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="single"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_30_output.mzML"/>
-      <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_32_input.mzML"/>
-      <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ginkgotoxin-ms-switching.raw"/>
-      <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":30"/>
-      <param name="mz" value=":1000"/>
-      <param name="int" value=":20000"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value="30:"/>
-      <param name="mz" value="1000:"/>
-      <param name="int" value="100:"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_4_input.mzML"/>
-      <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="true"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="rt" value=":1000"/>
-      <param name="mz" value=":480"/>
-      <param name="int" value=":79000"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":0.6"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":3"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="rt" value="1000:"/>
-      <param name="mz" value="440:"/>
-      <param name="int" value="70000:"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value="0.51:"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value="3:"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_7_input.mzML"/>
-      <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value="7000:"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_8_input.consensusXML"/>
-      <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="rt" value="600:1400"/>
-      <param name="mz" value="700:2300"/>
-      <param name="int" value="1100:6000"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_9_input.mzML"/>
-      <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value="SelectedIonMonitoring"/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_10_input.mzML"/>
-      <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value="Collision-induced dissociation"/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_11_input.mzML"/>
-      <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value="Plasma desorption"/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_12_input.mzML"/>
-      <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="true"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_13_input.consensusXML"/>
-      <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value="2"/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_14_input.consensusXML"/>
-      <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value="0 2"/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value="3000:4000"/>
-      <param name="mz" value="400:600"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value="3000:4000"/>
-      <param name="mz" value="400:600"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="true"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value="3000:4000"/>
-      <param name="mz" value="400:600"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="true"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value="&quot;YDL217C&quot;"/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="true"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="true"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value="&quot;distinct_charges&quot; &quot;gt&quot; &quot;1,2&quot;"/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value="&quot;distinct_charges_size&quot; &quot;gt&quot; &quot;2&quot;"/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value="&quot;DOESNOTEXIST&quot; &quot;lt&quot; &quot;whatever&quot;"/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="blacklist" value="FileFilter_25_input.idXML"/>
-        <param name="rt" value="1.0"/>
-        <param name="mz" value="0.05"/>
-        <param name="blacklist_imperfect" value="true"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="blacklist" value="FileFilter_25_input.idXML"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="true"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":2"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":2"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":35"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":35"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="false"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="linear"/>
-          <param name="lossy_mass_accuracy" value="0.0001"/>
-          <param name="intensity" value="slof"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="linear"/>
-          <param name="lossy_mass_accuracy" value="0.0001"/>
-          <param name="intensity" value="pic"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value="positive"/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value="negative"/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_43_input.mzML"/>
-      <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_43.tmp.mzML"/>
-      <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_44_input.mzML"/>
-      <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_45_input.featureXML"/>
-      <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_46_input.featureXML"/>
-      <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
-        <param name="sequence_comparison_method" value="exact"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="file" value="FileFilter_47_input_select.mzML"/>
-          <param name="similarity_threshold" value="0.9"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="file" value="FileFilter_47_input_select.mzML"/>
-          <param name="similarity_threshold" value="0.9"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="false"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_49_input.mzML"/>
-      <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="true"/>
-        <section name="numpress">
-          <param name="masstime" value="linear"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="pic"/>
-          <param name="float_da" value="slof"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileInfo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_1_input.dta" ftype="dta"/>
-      <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/>
-      <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_3_input.featureXML"/>
-      <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="true"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_4_input.mzXML"/>
-      <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_5_input.mzDat"/>
-      <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="false"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_6_input.mzData"/>
-      <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="true"/>
-      <param name="d" value="true"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_7_input.consensusXML"/>
-      <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="true"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_9_input.mzML"/>
-      <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="true"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_10_input.idXML"/>
-      <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_12_input.mzML"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_13_input.consensusXML"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_14_input.mzid"/>
-      <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="true"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_15_input.mzid"/>
-      <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="true"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_16_input.trafoXML"/>
-      <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_17_input.fasta"/>
-      <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_18_input.fasta"/>
-      <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileMerger">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value="5.0 10.0"/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="true"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="true"/>
-        <param name="ms_level" value="2"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/>
-      <param name="out_type" value="featureXML"/>
-      <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
-      <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/>
-      <param name="out_type" value="traML"/>
-      <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="10.0"/>
-      </section>
-      <output_collection name="rt_concat_trafo_out" count="2"/>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
-      <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_cols"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FuzzyDiff">
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
-        <param name="matched_whitelist" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
-      <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
-      <param name="ratio" value="1.01"/>
-      <param name="absdiff" value="0.01"/>
-      <param name="verbose" value="1"/>
-      <param name="tab_width" value="8"/>
-      <param name="first_column" value="1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_GNPSExport">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_single.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
-      <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="full_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_single.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
-      <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="merged_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
-      <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="full_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
-      <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="full_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_HighResPrecursorMassCorrector">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="4"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.2"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDConflictResolver">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_1_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="resolve_between_features" value="off"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_2_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="resolve_between_features" value="off"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_3_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="resolve_between_features" value="off"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_4_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="resolve_between_features" value="highest_intensity"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDExtractor">
-</xml>
-  <xml name="autotest_IDFileConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
-      <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PepXMLFile_test.pepxml"/>
-      <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="PepXMLFile_test.mzML"/>
-      <param name="mz_name" value="PepXMLFile_test"/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_3_input.protXML"/>
-      <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
-      <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_6_input1.pepXML"/>
-      <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
-      <param name="mz_name" value="F025589.dat.mzML"/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_7_input1.xml"/>
-      <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_8_input.mzid"/>
-      <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_9_input.idXML"/>
-      <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <param name="out_type" value="mzid"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_10_input.pepXML"/>
-      <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
-      <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="PEP"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="score"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
-      <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="spectra.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_16_input.pepXML"/>
-      <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_17_input.idXML"/>
-      <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_18_input.idXML"/>
-      <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_19_input.idXML"/>
-      <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_20_input.idXML"/>
-      <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_21_input.idXML"/>
-      <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDMapper_4_input.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.01"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
-      <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="spectra.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_23_input.mzid"/>
-      <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_24_input.pep.xml"/>
-      <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_25_input.idXML"/>
-      <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_26_input.mzid"/>
-      <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="-1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="true"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="true"/>
-        <param name="number_of_hits" value="2"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_31_input.mzid"/>
-      <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_1_input.idXML"/>
-      <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="proteins" value="IDFilter_1_input.fas"/>
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_3_input.idXML"/>
-      <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="peptides" value="IDFilter_3_2_input.idXML"/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_4_input.idXML"/>
-      <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.08"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="32.0"/>
-        <param name="prot" value="25.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="32.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="25.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="true"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="25.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_6_input.idXML"/>
-      <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="2"/>
-        <param name="n_protein_hits" value="10"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="true"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_7_input.idXML"/>
-      <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_8_input.idXML"/>
-      <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value="200:350"/>
-        <param name="mz" value="999:1000"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_9_input.idXML"/>
-      <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.05"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_10_input.idXML"/>
-      <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="true"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.3"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_11_input.idXML"/>
-      <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="true"/>
-      <param name="delete_unreferenced_peptide_hits" value="true"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_12_input.idXML"/>
-      <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_12_input.fasta"/>
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_13_input.idXML"/>
-      <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_13_input.fasta"/>
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_14_input.idXML"/>
-      <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_14_input.fasta"/>
-        <param name="enzyme" value="Trypsin/P"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_15_input.idXML"/>
-      <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_15_input.fasta"/>
-        <param name="enzyme" value="Trypsin/P"/>
-        <param name="specificity" value="semi"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_16_input.fasta"/>
-        <param name="enzyme" value="Trypsin/P"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="true"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":2"/>
-        <param name="enzyme" value="Lys-N"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value="2:"/>
-        <param name="enzyme" value="Lys-N"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value="1:3"/>
-        <param name="enzyme" value="Lys-N"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value="1:0"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value="&quot;calcMZ&quot; &quot;gt&quot; &quot;750.0&quot;"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value="&quot;end&quot; &quot;ne&quot; &quot;23&quot;"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMapper_2_output.consensusXML"/>
-      <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_3_out.consensusXML"/>
-      <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.99"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDMapper">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_1_input.idXML"/>
-      <param name="in" value="IDMapper_1_input.featureXML"/>
-      <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="5.0"/>
-      <param name="mz_tolerance" value="1.0"/>
-      <param name="mz_measure" value="Da"/>
-      <param name="mz_reference" value="precursor"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="false"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_2_input.idXML"/>
-      <param name="in" value="IDMapper_2_input.consensusXML"/>
-      <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="rt_tolerance" value="5.0"/>
-      <param name="mz_tolerance" value="1.0"/>
-      <param name="mz_measure" value="Da"/>
-      <param name="mz_reference" value="precursor"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_3_input.idXML"/>
-      <param name="in" value="IDMapper_3_input.featureXML"/>
-      <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="4.0"/>
-      <param name="mz_tolerance" value="3.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="precursor"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_4_input.idXML"/>
-      <param name="in" value="IDMapper_4_input.featureXML"/>
-      <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="10.0"/>
-      <param name="mz_tolerance" value="20.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_4_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_5_input.idXML"/>
-      <param name="in" value="IDMapper_5_input.featureXML"/>
-      <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="20.0"/>
-      <param name="mz_tolerance" value="10.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="false"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_5_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDMassAccuracy">
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="number_of_bins" value="10"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
-      <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_error_ppm" value="false"/>
-      <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_error_ppm" value="false"/>
-      <param name="fragment_mass_tolerance" value="0.5"/>
-      <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDMerger">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
-      <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="true"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
-      <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="true"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
-      <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
-      <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_2_input1.idXML"/>
-      <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="add_to" value="IDMerger_5_input1.idXML"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
-      <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="true"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDPosteriorErrorProbability">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="true"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="true"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="true"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="true"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="true"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDRipper"/>
-  <xml name="autotest_IDRTCalibration">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDRTCalibration_1_input.idXML"/>
-      <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="calibrant_1_reference" value="0.1"/>
-      <param name="calibrant_2_reference" value="0.9"/>
-      <param name="calibrant_1_input" value="10.0"/>
-      <param name="calibrant_2_input" value="90.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="degenerated_empty.idXML"/>
-      <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="calibrant_1_reference" value="0.1"/>
-      <param name="calibrant_2_reference" value="0.9"/>
-      <param name="calibrant_1_input" value="10.0"/>
-      <param name="calibrant_2_input" value="90.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDScoreSwitcher">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_output.idXML"/>
-      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="proteins" value="false"/>
-      <param name="new_score" value="Percolator_PEP"/>
-      <param name="new_score_orientation" value="lower_better"/>
-      <param name="new_score_type" value="Posterior Error Probability"/>
-      <param name="old_score" value="Percolator_qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
-      <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="proteins" value="true"/>
-      <param name="new_score" value="Posterior Probability_score"/>
-      <param name="new_score_orientation" value="higher_better"/>
-      <param name="new_score_type" value="Posterior Probability"/>
-      <param name="old_score" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDSplitter">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMapper_1_output.featureXML"/>
-      <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_InternalCalibration">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
-      <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ppm_match_tolerance" value="25.0"/>
-      <param name="ms_level" value="1"/>
-      <param name="RT_chunking" value="-1.0"/>
-      <section name="cal">
-        <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
-        <param name="lock_require_mono" value="false"/>
-        <param name="lock_require_iso" value="false"/>
-        <param name="model_type" value="linear"/>
-      </section>
-      <section name="RANSAC">
-        <param name="enabled" value="true"/>
-        <param name="threshold" value="1.0"/>
-        <param name="pc_inliers" value="30"/>
-        <param name="iter" value="500"/>
-      </section>
-      <section name="goodness">
-        <param name="median" value="4.0"/>
-        <param name="MAD" value="2.0"/>
-      </section>
-      <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
-      <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ppm_match_tolerance" value="25.0"/>
-      <param name="ms_level" value="1 2 3"/>
-      <param name="RT_chunking" value="60.0"/>
-      <section name="cal">
-        <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
-        <param name="lock_require_mono" value="true"/>
-        <param name="lock_require_iso" value="false"/>
-        <param name="model_type" value="linear"/>
-      </section>
-      <section name="RANSAC">
-        <param name="enabled" value="false"/>
-        <param name="threshold" value="10.0"/>
-        <param name="pc_inliers" value="30"/>
-        <param name="iter" value="70"/>
-      </section>
-      <section name="goodness">
-        <param name="median" value="4.0"/>
-        <param name="MAD" value="2.0"/>
-      </section>
-      <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IsobaricAnalyzer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="itraq4plex"/>
-      <param name="in" value="IsobaricAnalyzer_input_1.mzML"/>
-      <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value=""/>
-        <param name="reporter_mass_shift" value="0.1"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value="l1"/>
-        <param name="channel_115_description" value="l2"/>
-        <param name="channel_116_description" value="l3"/>
-        <param name="channel_117_description" value="lung"/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="itraq4plex"/>
-      <param name="in" value="TMTTenPlexMethod_test.mzML"/>
-      <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value="High-energy collision-induced dissociation"/>
-        <param name="reporter_mass_shift" value="0.002"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/5.0/0.0&quot; &quot;0.0/0.2/4.6/0.0&quot; &quot;0.0/0.2/4.6/0.3&quot; &quot;0.0/0.9/4.7/0.2&quot; &quot;0.0/0.5/3.2/0.0&quot; &quot;0.0/0.7/3.3/0.0&quot; &quot;0.0/1.3/2.5/0.0&quot; &quot;0.0/1.2/2.8/2.7&quot; &quot;0.0/1.5/2.0/0.0&quot; &quot;0.0/1.5/1.9/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="itraq4plex"/>
-      <param name="in" value="TMTTenPlexMethod_test.mzML"/>
-      <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value="High-energy collision-induced dissociation"/>
-        <param name="reporter_mass_shift" value="0.002"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="tmt10plex"/>
-      <param name="in" value="MS3_nonHierarchical.mzML"/>
-      <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value="Collision-induced dissociation"/>
-        <param name="reporter_mass_shift" value="0.002"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/5.09/0.0&quot; &quot;0.0/0.25/5.27/0.0&quot; &quot;0.0/0.37/5.36/0.15&quot; &quot;0.0/0.65/4.17/0.1&quot; &quot;0.08/0.49/3.06/0.0&quot; &quot;0.01/0.71/3.07/0.0&quot; &quot;0.0/1.32/2.62/0.0&quot; &quot;0.02/1.28/2.75/2.53&quot; &quot;0.03/2.08/2.23/0.0&quot; &quot;0.08/1.99/1.65/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_LabeledEval">
-</xml>
-  <xml name="autotest_LuciphorAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="LuciphorAdapter_1_input.mzML"/>
-      <param name="id" value="LuciphorAdapter_1_input.idXML"/>
-      <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="fragment_method" value="CID"/>
-      <param name="fragment_mass_tolerance" value="0.5"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="min_mz" value="150.0"/>
-      <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/>
-      <param name="neutral_losses" value="&quot;sty -H3PO4 -97.97690&quot;"/>
-      <param name="decoy_mass" value="79.966331"/>
-      <param name="decoy_neutral_losses" value="&quot;X -H3PO4 -97.97690&quot;"/>
-      <param name="max_charge_state" value="5"/>
-      <param name="max_peptide_length" value="40"/>
-      <param name="max_num_perm" value="16384"/>
-      <param name="modeling_score_threshold" value="0.95"/>
-      <param name="scoring_threshold" value="0.0"/>
-      <param name="min_num_psms_model" value="1"/>
-      <param name="run_mode" value="0"/>
-      <param name="rt_tolerance" value="0.01"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerIdentification">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
-      <output_collection name="out" count="1"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="1"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="2"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
-      <output_collection name="trafo_out" count="1"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
-      <output_collection name="out" count="1"/>
-      <output_collection name="trafo_out" count="1"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.5"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerPoseClustering">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
-      <output_collection name="out" count="3"/>
-      <output_collection name="trafo_out" count="3"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="true"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="30.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/>
-      <output_collection name="out" count="3"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="false"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="100.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="true"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="30.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/>
-      <output_collection name="trafo_out" count="2"/>
-      <section name="reference">
-        <param name="index" value="2"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="true"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="30.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerSpectrum">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/>
-      <output_collection name="out" count="3"/>
-      <section name="algorithm">
-        <param name="gapcost" value="1.0"/>
-        <param name="affinegapcost" value="0.5"/>
-        <param name="cutoff_score" value="0.7"/>
-        <param name="bucketsize" value="100"/>
-        <param name="anchorpoints" value="100"/>
-        <param name="mismatchscore" value="-5.0"/>
-        <param name="scorefunction" value="SteinScottImproveScore"/>
-      </section>
-      <section name="model">
-        <param name="type" value="interpolated"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerTreeGuided">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
-      <output_collection name="out" count="3"/>
-      <section name="algorithm">
-        <param name="model_type" value="b_spline"/>
-        <section name="model">
-          <param name="type" value="b_spline"/>
-          <section name="linear">
-            <param name="symmetric_regression" value="false"/>
-            <param name="x_weight" value=""/>
-            <param name="y_weight" value=""/>
-            <param name="x_datum_min" value="1e-15"/>
-            <param name="x_datum_max" value="1000000000000000.0"/>
-            <param name="y_datum_min" value="1e-15"/>
-            <param name="y_datum_max" value="1000000000000000.0"/>
-          </section>
-          <section name="b_spline">
-            <param name="wavelength" value="0.0"/>
-            <param name="num_nodes" value="5"/>
-            <param name="extrapolate" value="linear"/>
-            <param name="boundary_condition" value="2"/>
-          </section>
-          <section name="lowess">
-            <param name="span" value="0.666666666666667"/>
-            <param name="num_iterations" value="3"/>
-            <param name="delta" value="-1.0"/>
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="four-point-linear"/>
-          </section>
-          <section name="interpolated">
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="two-point-linear"/>
-          </section>
-        </section>
-        <section name="align_algorithm">
-          <param name="score_cutoff" value="false"/>
-          <param name="min_score" value="0.05"/>
-          <param name="min_run_occur" value="2"/>
-          <param name="max_rt_shift" value="0.5"/>
-          <param name="use_unassigned_peptides" value="true"/>
-          <param name="use_feature_rt" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
-      <output_collection name="trafo_out" count="3"/>
-      <section name="algorithm">
-        <param name="model_type" value="b_spline"/>
-        <section name="model">
-          <param name="type" value="b_spline"/>
-          <section name="linear">
-            <param name="symmetric_regression" value="false"/>
-            <param name="x_weight" value=""/>
-            <param name="y_weight" value=""/>
-            <param name="x_datum_min" value="1e-15"/>
-            <param name="x_datum_max" value="1000000000000000.0"/>
-            <param name="y_datum_min" value="1e-15"/>
-            <param name="y_datum_max" value="1000000000000000.0"/>
-          </section>
-          <section name="b_spline">
-            <param name="wavelength" value="0.0"/>
-            <param name="num_nodes" value="5"/>
-            <param name="extrapolate" value="linear"/>
-            <param name="boundary_condition" value="2"/>
-          </section>
-          <section name="lowess">
-            <param name="span" value="0.666666666666667"/>
-            <param name="num_iterations" value="3"/>
-            <param name="delta" value="-1.0"/>
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="four-point-linear"/>
-          </section>
-          <section name="interpolated">
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="two-point-linear"/>
-          </section>
-        </section>
-        <section name="align_algorithm">
-          <param name="score_cutoff" value="false"/>
-          <param name="min_score" value="0.05"/>
-          <param name="min_run_occur" value="2"/>
-          <param name="max_rt_shift" value="0.5"/>
-          <param name="use_unassigned_peptides" value="true"/>
-          <param name="use_feature_rt" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
-      <output_collection name="out" count="3"/>
-      <section name="algorithm">
-        <param name="model_type" value="b_spline"/>
-        <section name="model">
-          <param name="type" value="b_spline"/>
-          <section name="linear">
-            <param name="symmetric_regression" value="false"/>
-            <param name="x_weight" value=""/>
-            <param name="y_weight" value=""/>
-            <param name="x_datum_min" value="1e-15"/>
-            <param name="x_datum_max" value="1000000000000000.0"/>
-            <param name="y_datum_min" value="1e-15"/>
-            <param name="y_datum_max" value="1000000000000000.0"/>
-          </section>
-          <section name="b_spline">
-            <param name="wavelength" value="0.0"/>
-            <param name="num_nodes" value="5"/>
-            <param name="extrapolate" value="linear"/>
-            <param name="boundary_condition" value="2"/>
-          </section>
-          <section name="lowess">
-            <param name="span" value="0.666666666666667"/>
-            <param name="num_iterations" value="3"/>
-            <param name="delta" value="-1.0"/>
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="four-point-linear"/>
-          </section>
-          <section name="interpolated">
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="two-point-linear"/>
-          </section>
-        </section>
-        <section name="align_algorithm">
-          <param name="score_cutoff" value="false"/>
-          <param name="min_score" value="0.05"/>
-          <param name="min_run_occur" value="2"/>
-          <param name="max_rt_shift" value="0.5"/>
-          <param name="use_unassigned_peptides" value="true"/>
-          <param name="use_feature_rt" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapNormalizer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_input.mzML"/>
-      <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapRTTransformer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_2_input.mzML"/>
-      <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
-      <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="invert" value="true"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
-      <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="true"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapStatistics">
-</xml>
-  <xml name="autotest_MaRaClusterAdapter"/>
-  <xml name="autotest_MascotAdapterOnline">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_protein_links" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="Mascot_parameters">
-        <param name="database" value="SwissProt"/>
-        <param name="search_type" value="MIS"/>
-        <param name="enzyme" value="Trypsin"/>
-        <param name="instrument" value="Default"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="precursor_mass_tolerance" value="3.0"/>
-        <param name="precursor_error_units" value="Da"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="fragment_error_units" value="Da"/>
-        <param name="charges" value="1,2,3"/>
-        <param name="taxonomy" value="All entries"/>
-        <param name="fixed_modifications" value=""/>
-        <param name="variable_modifications" value=""/>
-        <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/>
-        <param name="mass_type" value="monoisotopic"/>
-        <param name="number_of_hits" value="0"/>
-        <param name="skip_spectrum_charges" value="false"/>
-        <param name="search_title" value="OpenMS_search"/>
-        <param name="username" value="OpenMS"/>
-        <param name="email" value="openmsjenkins@gmail.com"/>
-      </section>
-      <section name="Mascot_server">
-        <param name="hostname" value="www.matrixscience.com"/>
-        <param name="host_port" value="80"/>
-        <param name="server_path" value=""/>
-        <param name="timeout" value="1500"/>
-        <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/>
-        <param name="use_proxy" value="false"/>
-        <param name="proxy_host" value=""/>
-        <param name="proxy_port" value="0"/>
-        <param name="proxy_username" value=""/>
-        <param name="proxy_password" value=""/>
-        <param name="login" value="false"/>
-        <param name="username" value=""/>
-        <param name="password" value=""/>
-        <param name="use_ssl" value="false"/>
-        <param name="export_params" value="_ignoreionsscorebelow=0&amp;_sigthreshold=0.99&amp;_showsubsets=1&amp;show_same_sets=1&amp;report=0&amp;percolate=0&amp;query_master=0"/>
-        <param name="skip_export" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MascotAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MascotAdapter_1_input.mzData"/>
-      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mgf"/>
-      <param name="instrument" value="ESI-TRAP"/>
-      <param name="precursor_mass_tolerance" value="1.3"/>
-      <param name="peak_mass_tolerance" value="0.3"/>
-      <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
-      <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
-      <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
-      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
-      <param name="db" value="MSDB"/>
-      <param name="hits" value="AUTO"/>
-      <param name="cleavage" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="sig_threshold" value="0.05"/>
-      <param name="pep_homol" value="1.0"/>
-      <param name="pep_ident" value="1.0"/>
-      <param name="pep_rank" value="1"/>
-      <param name="prot_score" value="1.0"/>
-      <param name="pep_score" value="1.0"/>
-      <param name="pep_exp_z" value="1"/>
-      <param name="show_unassigned" value="1"/>
-      <param name="first_dim_rt" value="0.0"/>
-      <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
-      <param name="mass_type" value="Monoisotopic"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MascotAdapter_2_input.mascotXML"/>
-      <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="instrument" value="Default"/>
-      <param name="precursor_mass_tolerance" value="2.0"/>
-      <param name="peak_mass_tolerance" value="1.0"/>
-      <param name="taxonomy" value="All entries"/>
-      <param name="modifications" value=""/>
-      <param name="variable_modifications" value=""/>
-      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
-      <param name="db" value="MSDB"/>
-      <param name="hits" value="AUTO"/>
-      <param name="cleavage" value="Trypsin"/>
-      <param name="missed_cleavages" value="0"/>
-      <param name="sig_threshold" value="0.05"/>
-      <param name="pep_homol" value="1.0"/>
-      <param name="pep_ident" value="1.0"/>
-      <param name="pep_rank" value="1"/>
-      <param name="prot_score" value="1.0"/>
-      <param name="pep_score" value="1.0"/>
-      <param name="pep_exp_z" value="1"/>
-      <param name="show_unassigned" value="1"/>
-      <param name="first_dim_rt" value="0.0"/>
-      <param name="boundary" value=""/>
-      <param name="mass_type" value="Monoisotopic"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MassCalculator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
-      <param name="in_seq" value=""/>
-      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="charge" value="0 1"/>
-      <param name="format" value="table"/>
-      <param name="average_mass" value="false"/>
-      <param name="fragment_type" value="full"/>
-      <param name="separator" value=","/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
-      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="charge" value="1 2 3"/>
-      <param name="format" value="list"/>
-      <param name="average_mass" value="false"/>
-      <param name="fragment_type" value="full"/>
-      <param name="separator" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MassTraceExtractor">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MassTraceExtractor_1_input.mzML"/>
-      <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="-1.0"/>
-        </section>
-        <section name="epd">
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-          <param name="enabled" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MassTraceExtractor_1_input.mzML"/>
-      <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="6.0"/>
-          <param name="max_trace_length" value="12.0"/>
-        </section>
-        <section name="epd">
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-          <param name="enabled" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MetaboliteAdductDecharger">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
-      <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="MetaboliteFeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="3"/>
-          <param name="charge_span_max" value="3"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.05"/>
-          <param name="unit" value="Da"/>
-          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
-          <param name="max_neutrals" value="1"/>
-          <param name="use_minority_bound" value="true"/>
-          <param name="max_minority_bound" value="3"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
-      <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <section name="MetaboliteFeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="3"/>
-          <param name="charge_span_max" value="3"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.05"/>
-          <param name="unit" value="Da"/>
-          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
-          <param name="max_neutrals" value="1"/>
-          <param name="use_minority_bound" value="true"/>
-          <param name="max_minority_bound" value="3"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MetaboliteSpectralMatcher">
-</xml>
-  <xml name="autotest_MetaProSIP">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_correlation_distance_to_averagine" value="-1.0"/>
-        <param name="pattern_15N_TIC_threshold" value="0.95"/>
-        <param name="pattern_13C_TIC_threshold" value="0.95"/>
-        <param name="pattern_2H_TIC_threshold" value="0.95"/>
-        <param name="pattern_18O_TIC_threshold" value="0.95"/>
-        <param name="heatmap_bins" value="20"/>
-        <param name="observed_peak_fraction" value="0.5"/>
-        <param name="min_consecutive_isotopes" value="2"/>
-        <param name="score_plot_yaxis_min" value="0.0"/>
-        <param name="collect_method" value="correlation_maximum"/>
-        <param name="lowRIA_correlation_threshold" value="-1.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
-      <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
-      <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
-      <param name="mz_tolerance_ppm" value="10.0"/>
-      <param name="rt_tolerance_s" value="30.0"/>
-      <param name="intensity_threshold" value="10.0"/>
-      <param name="correlation_threshold" value="0.7"/>
-      <param name="xic_threshold" value="0.7"/>
-      <param name="decomposition_threshold" value="0.7"/>
-      <param name="weight_merge_window" value="5.0"/>
-      <param name="plot_extension" value="png"/>
-      <param name="qc_output_directory" value=""/>
-      <param name="labeling_element" value="C"/>
-      <param name="use_unassigned_ids" value="false"/>
-      <param name="use_averagine_ids" value="false"/>
-      <param name="report_natural_peptides" value="false"/>
-      <param name="filter_monoisotopic" value="false"/>
-      <param name="cluster" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MRMMapper">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMMapping_input.chrom.mzML"/>
-      <param name="tr" value="MRMMapping_input.TraML"/>
-      <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="precursor_tolerance" value="0.3"/>
-        <param name="product_tolerance" value="0.3"/>
-        <param name="map_multiple_assays" value="false"/>
-        <param name="error_on_unmapped" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMMapping_input.chrom.mzML"/>
-      <param name="tr" value="MRMMapping_input_2.TraML"/>
-      <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="precursor_tolerance" value="0.01"/>
-        <param name="product_tolerance" value="0.01"/>
-        <param name="map_multiple_assays" value="false"/>
-        <param name="error_on_unmapped" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MRMPairFinder">
-</xml>
-  <xml name="autotest_MRMTransitionGroupPicker">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
-      <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
-      <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="stop_after_feature" value="-1"/>
-        <param name="stop_after_intensity_ratio" value="0.0001"/>
-        <param name="min_peak_width" value="-1.0"/>
-        <param name="peak_integration" value="original"/>
-        <param name="background_subtraction" value="none"/>
-        <param name="recalculate_peaks" value="false"/>
-        <param name="use_precursors" value="false"/>
-        <param name="use_consensus" value="true"/>
-        <param name="recalculate_peaks_max_z" value="1.0"/>
-        <param name="minimal_quality" value="-10000.0"/>
-        <param name="resample_boundary" value="15.0"/>
-        <param name="compute_peak_quality" value="false"/>
-        <param name="compute_peak_shape_metrics" value="false"/>
-        <param name="compute_total_mi" value="false"/>
-        <param name="boundary_selection_method" value="largest"/>
-        <section name="PeakPickerMRM">
-          <param name="sgolay_frame_length" value="15"/>
-          <param name="sgolay_polynomial_order" value="3"/>
-          <param name="gauss_width" value="50.0"/>
-          <param name="use_gauss" value="true"/>
-          <param name="peak_width" value="40.0"/>
-          <param name="signal_to_noise" value="1.0"/>
-          <param name="sn_win_len" value="1000.0"/>
-          <param name="sn_bin_count" value="30"/>
-          <param name="write_sn_log_messages" value="false"/>
-          <param name="remove_overlapping_peaks" value="true"/>
-          <param name="method" value="legacy"/>
-        </section>
-        <section name="PeakIntegrator">
-          <param name="integration_type" value="intensity_sum"/>
-          <param name="baseline_type" value="base_to_base"/>
-          <param name="fit_EMG" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
-      <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
-      <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="stop_after_feature" value="-1"/>
-        <param name="stop_after_intensity_ratio" value="0.0001"/>
-        <param name="min_peak_width" value="-1.0"/>
-        <param name="peak_integration" value="original"/>
-        <param name="background_subtraction" value="none"/>
-        <param name="recalculate_peaks" value="false"/>
-        <param name="use_precursors" value="false"/>
-        <param name="use_consensus" value="true"/>
-        <param name="recalculate_peaks_max_z" value="1.0"/>
-        <param name="minimal_quality" value="-10000.0"/>
-        <param name="resample_boundary" value="15.0"/>
-        <param name="compute_peak_quality" value="false"/>
-        <param name="compute_peak_shape_metrics" value="false"/>
-        <param name="compute_total_mi" value="true"/>
-        <param name="boundary_selection_method" value="largest"/>
-        <section name="PeakPickerMRM">
-          <param name="sgolay_frame_length" value="15"/>
-          <param name="sgolay_polynomial_order" value="3"/>
-          <param name="gauss_width" value="50.0"/>
-          <param name="use_gauss" value="true"/>
-          <param name="peak_width" value="40.0"/>
-          <param name="signal_to_noise" value="1.0"/>
-          <param name="sn_win_len" value="1000.0"/>
-          <param name="sn_bin_count" value="30"/>
-          <param name="write_sn_log_messages" value="false"/>
-          <param name="remove_overlapping_peaks" value="true"/>
-          <param name="method" value="legacy"/>
-        </section>
-        <section name="PeakIntegrator">
-          <param name="integration_type" value="intensity_sum"/>
-          <param name="baseline_type" value="base_to_base"/>
-          <param name="fit_EMG" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MSFraggerAdapter"/>
-  <xml name="autotest_MSGFPlusAdapter">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="add_decoys" value="false"/>
-        <param name="legacy_conversion" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="precursor_mass_tolerance" value="10.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error_range" value="0,1"/>
-      <param name="fragment_method" value="from_spectrum"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin/P"/>
-      <param name="protocol" value="none"/>
-      <param name="tryptic" value="fully"/>
-      <param name="min_precursor_charge" value="1"/>
-      <param name="max_precursor_charge" value="3"/>
-      <param name="min_peptide_length" value="6"/>
-      <param name="max_peptide_length" value="40"/>
-      <param name="matches_per_spec" value="1"/>
-      <param name="add_features" value="false"/>
-      <param name="max_mods" value="2"/>
-      <param name="max_missed_cleavages" value="-1"/>
-      <param name="tasks" value="0"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MSSimulator">
-</xml>
-  <xml name="autotest_MSstatsConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="retention_time_summarization_method" value="max"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSstatsConverter_1_in.consensusXML"/>
-      <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/>
-      <param name="method" value="LFQ"/>
-      <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
-      <param name="msstats_condition" value="MSstats_Condition"/>
-      <param name="msstats_mixture" value="MSstats_Mixture"/>
-      <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="retention_time_summarization_method" value="manual"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSstatsConverter_2_in.consensusXML"/>
-      <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/>
-      <param name="method" value="ISO"/>
-      <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
-      <param name="msstats_condition" value="MSstats_Condition"/>
-      <param name="msstats_mixture" value="MSstats_Mixture"/>
-      <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="retention_time_summarization_method" value="manual"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
-      <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/>
-      <param name="method" value="ISO"/>
-      <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
-      <param name="msstats_condition" value="MSstats_Condition"/>
-      <param name="msstats_mixture" value="MSstats_Mixture"/>
-      <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MultiplexResolver">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="5"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
-        <param name="missed_cleavages" value="4"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="5"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Leu3]"/>
-        <param name="missed_cleavages" value="2"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="5"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
-      <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
-      <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="10"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MyriMatchAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="MinPeptideMass" value="0.0"/>
-        <param name="MaxPeptideMass" value="10000.0"/>
-        <param name="MinPeptideLength" value="5"/>
-        <param name="MaxPeptideLength" value="75"/>
-        <param name="UseSmartPlusThreeModel" value="false"/>
-        <param name="NumIntensityClasses" value="3"/>
-        <param name="ClassSizeMultiplier" value="2.0"/>
-        <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/>
-        <param name="SpectrumListFilters" value=""/>
-        <param name="ignoreConfigErrors" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_mass_tolerance_unit" value="ppm"/>
-      <param name="precursor_mass_tolerance_avg" value="false"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="fragment_mass_tolerance_unit" value="Da"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="NumChargeStates" value="3"/>
-      <param name="TicCutoffPercentage" value="0.98"/>
-      <param name="MaxDynamicMods" value="2"/>
-      <param name="MaxResultRank" value="5"/>
-      <param name="CleavageRules" value=""/>
-      <param name="MinTerminiCleavages" value="2"/>
-      <param name="MaxMissedCleavages" value="-1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MzMLSplitter"/>
-  <xml name="autotest_MzTabExporter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_1_input.consensusXML"/>
-      <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_2_input.idXML"/>
-      <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_3_input.featureXML"/>
-      <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_2_out.consensusXML"/>
-      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_5_in.consensusXML"/>
-      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_6_input.idXML"/>
-      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_7_input.consensusXML"/>
-      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_NoiseFilterGaussian">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="1.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="50.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="1.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="50.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_NoiseFilterSGolay">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="9"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="11"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="9"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="11"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_NovorAdapter"/>
-  <xml name="autotest_NucleicAcidSearchEngine">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="decharge_ms2" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
-      <param name="database" value="NucleicAcidSearchEngine_1.fasta"/>
-      <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="5.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="-2"/>
-        <param name="max_charge" value="-14"/>
-        <param name="include_unknown_charge" value="true"/>
-        <param name="use_avg_mass" value="false"/>
-        <param name="use_adducts" value="false"/>
-        <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
-        <param name="isotopes" value="0 1 2"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="5.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="ions" value="a-B,c,w,y"/>
-      </section>
-      <section name="modifications">
-        <param name="variable" value=""/>
-        <param name="variable_max_per_oligo" value="2"/>
-        <param name="resolve_ambiguities" value="false"/>
-      </section>
-      <section name="oligo">
-        <param name="min_size" value="5"/>
-        <param name="max_size" value="0"/>
-        <param name="missed_cleavages" value="22"/>
-        <param name="enzyme" value="no cleavage"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="1"/>
-      </section>
-      <section name="fdr">
-        <param name="decoy_pattern" value="DECOY_"/>
-        <param name="cutoff" value="0.05"/>
-        <param name="remove_decoys" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OMSSAAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="pc" value="1"/>
-        <param name="hs" value="4"/>
-        <param name="tez" value="1"/>
-        <param name="tom" value="0"/>
-        <param name="tem" value="0"/>
-        <param name="tex" value="1446.94"/>
-        <param name="zt" value="3"/>
-        <param name="z1" value="0.95"/>
-        <param name="zc" value="1"/>
-        <param name="zcc" value="2"/>
-        <param name="zoh" value="2"/>
-        <param name="no" value="4"/>
-        <param name="nox" value="40"/>
-        <param name="i" value="1,4"/>
-        <param name="sp" value="100"/>
-        <param name="sb1" value="1"/>
-        <param name="sct" value="0"/>
-        <param name="x" value="0"/>
-        <param name="hm" value="2"/>
-        <param name="ht" value="6"/>
-        <param name="mm" value="128"/>
-        <param name="mnm" value="false"/>
-        <param name="is" value="0.0"/>
-        <param name="ir" value="0.0"/>
-        <param name="ii" value="0.0"/>
-        <param name="chunk_size" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="min_precursor_charge" value="1"/>
-      <param name="max_precursor_charge" value="3"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="v" value="1"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="hl" value="30"/>
-      <param name="he" value="1.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenPepXLLF">
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenPepXLLF_input.mzML"/>
-      <param name="database" value="OpenPepXLLF_input.fasta"/>
-      <param name="decoy_string" value="decoy"/>
-      <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="3"/>
-        <param name="max_charge" value="7"/>
-        <param name="corrections" value="2 1 0"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_xlinks" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="5"/>
-        <param name="missed_cleavages" value="2"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="cross_linker">
-        <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="mass" value="138.0680796"/>
-        <param name="mass_mono_link" value="156.07864431 155.094628715"/>
-        <param name="name" value="DSS"/>
-      </section>
-      <section name="algorithm">
-        <param name="number_top_hits" value="5"/>
-        <param name="deisotope" value="auto"/>
-        <param name="use_sequence_tags" value="false"/>
-        <param name="sequence_tag_min_length" value="2"/>
-      </section>
-      <section name="ions">
-        <param name="b_ions" value="true"/>
-        <param name="y_ions" value="true"/>
-        <param name="a_ions" value="false"/>
-        <param name="x_ions" value="false"/>
-        <param name="c_ions" value="false"/>
-        <param name="z_ions" value="false"/>
-        <param name="neutral_losses" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenPepXLLF_input2.mzML"/>
-      <param name="database" value="OpenPepXLLF_input2.fasta"/>
-      <param name="decoy_string" value="decoy_"/>
-      <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="3"/>
-        <param name="max_charge" value="7"/>
-        <param name="corrections" value="1 0"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="0.2"/>
-        <param name="mass_tolerance_xlinks" value="0.3"/>
-        <param name="mass_tolerance_unit" value="Da"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value="Carbamidomethyl (C)"/>
-        <param name="variable" value="Oxidation (M)"/>
-        <param name="variable_max_per_peptide" value="1"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="5"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="cross_linker">
-        <param name="residue1" value="&quot;D&quot; &quot;E&quot; &quot;C-term&quot;"/>
-        <param name="residue2" value="&quot;K&quot; &quot;S&quot; &quot;T&quot; &quot;Y&quot; &quot;N-term&quot;"/>
-        <param name="mass" value="-18.010595"/>
-        <param name="mass_mono_link" value=""/>
-        <param name="name" value="DMTMM"/>
-      </section>
-      <section name="algorithm">
-        <param name="number_top_hits" value="1"/>
-        <param name="deisotope" value="auto"/>
-        <param name="use_sequence_tags" value="false"/>
-        <param name="sequence_tag_min_length" value="2"/>
-      </section>
-      <section name="ions">
-        <param name="b_ions" value="true"/>
-        <param name="y_ions" value="true"/>
-        <param name="a_ions" value="false"/>
-        <param name="x_ions" value="false"/>
-        <param name="c_ions" value="false"/>
-        <param name="z_ions" value="false"/>
-        <param name="neutral_losses" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenPepXL">
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenPepXL_input.mzML"/>
-      <param name="consensus" value="OpenPepXL_input.consensusXML"/>
-      <param name="database" value="OpenPepXL_input.fasta"/>
-      <param name="decoy_string" value="decoy"/>
-      <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="3"/>
-        <param name="max_charge" value="7"/>
-        <param name="corrections" value="2 1 0"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="0.2"/>
-        <param name="mass_tolerance_xlinks" value="0.3"/>
-        <param name="mass_tolerance_unit" value="Da"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="5"/>
-        <param name="missed_cleavages" value="2"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="cross_linker">
-        <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="mass_light" value="138.0680796"/>
-        <param name="mass_iso_shift" value="12.075321"/>
-        <param name="mass_mono_link" value="156.07864431 155.094628715"/>
-        <param name="name" value="DSS"/>
-      </section>
-      <section name="algorithm">
-        <param name="number_top_hits" value="5"/>
-        <param name="deisotope" value="auto"/>
-      </section>
-      <section name="ions">
-        <param name="b_ions" value="true"/>
-        <param name="y_ions" value="true"/>
-        <param name="a_ions" value="false"/>
-        <param name="x_ions" value="false"/>
-        <param name="c_ions" value="false"/>
-        <param name="z_ions" value="false"/>
-        <param name="neutral_losses" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathAnalyzer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="true"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="8.0"/>
-          <param name="dia_byseries_ppm_diff" value="15.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="true"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="8.0"/>
-          <param name="dia_byseries_ppm_diff" value="15.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="original"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="true"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathAssayGenerator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_num_alternative_localizations" value="10000"/>
-        <param name="disable_identification_ms2_precursors" value="false"/>
-        <param name="disable_identification_specific_losses" value="false"/>
-        <param name="enable_identification_unspecific_losses" value="false"/>
-        <param name="enable_swath_specifity" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="min_transitions" value="6"/>
-      <param name="max_transitions" value="6"/>
-      <param name="allowed_fragment_types" value="b,y"/>
-      <param name="allowed_fragment_charges" value="2,3"/>
-      <param name="enable_detection_specific_losses" value="true"/>
-      <param name="enable_detection_unspecific_losses" value="false"/>
-      <param name="precursor_mz_threshold" value="0.025"/>
-      <param name="precursor_lower_mz_limit" value="400.0"/>
-      <param name="precursor_upper_mz_limit" value="1200.0"/>
-      <param name="product_mz_threshold" value="0.025"/>
-      <param name="product_lower_mz_limit" value="350.0"/>
-      <param name="product_upper_mz_limit" value="2000.0"/>
-      <param name="enable_ipf" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_num_alternative_localizations" value="10000"/>
-        <param name="disable_identification_ms2_precursors" value="false"/>
-        <param name="disable_identification_specific_losses" value="false"/>
-        <param name="enable_identification_unspecific_losses" value="false"/>
-        <param name="enable_swath_specifity" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="min_transitions" value="6"/>
-      <param name="max_transitions" value="6"/>
-      <param name="allowed_fragment_types" value="b,y"/>
-      <param name="allowed_fragment_charges" value="1,2,3,4"/>
-      <param name="enable_detection_specific_losses" value="false"/>
-      <param name="enable_detection_unspecific_losses" value="false"/>
-      <param name="precursor_mz_threshold" value="0.025"/>
-      <param name="precursor_lower_mz_limit" value="400.0"/>
-      <param name="precursor_upper_mz_limit" value="1200.0"/>
-      <param name="product_mz_threshold" value="0.025"/>
-      <param name="product_lower_mz_limit" value="350.0"/>
-      <param name="product_upper_mz_limit" value="2000.0"/>
-      <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/>
-      <param name="enable_ipf" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_num_alternative_localizations" value="10000"/>
-        <param name="disable_identification_ms2_precursors" value="false"/>
-        <param name="disable_identification_specific_losses" value="false"/>
-        <param name="enable_identification_unspecific_losses" value="false"/>
-        <param name="enable_swath_specifity" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="min_transitions" value="6"/>
-      <param name="max_transitions" value="6"/>
-      <param name="allowed_fragment_types" value="b,y"/>
-      <param name="allowed_fragment_charges" value="1,2,3,4"/>
-      <param name="enable_detection_specific_losses" value="false"/>
-      <param name="enable_detection_unspecific_losses" value="false"/>
-      <param name="precursor_mz_threshold" value="0.025"/>
-      <param name="precursor_lower_mz_limit" value="400.0"/>
-      <param name="precursor_upper_mz_limit" value="1200.0"/>
-      <param name="product_mz_threshold" value="0.025"/>
-      <param name="product_lower_mz_limit" value="350.0"/>
-      <param name="product_upper_mz_limit" value="2000.0"/>
-      <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/>
-      <param name="enable_ipf" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathChromatogramExtractor">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="false"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="50.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="false"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="true"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="true"/>
-      <param name="extract_MS1" value="false"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="true"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathConfidenceScoring">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
-      <param name="decoys" value="1"/>
-      <param name="transitions" value="2"/>
-      <section name="GLM">
-        <param name="intercept" value="3.87333466"/>
-        <param name="delta_rt" value="-0.02898629"/>
-        <param name="dist_int" value="-7.75880768"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathDecoyGenerator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.8"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.025"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="false"/>
-        <param name="enable_detection_unspecific_losses" value="false"/>
-        <param name="separate" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.8"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.8"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="false"/>
-        <param name="enable_detection_unspecific_losses" value="false"/>
-        <param name="separate" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.8"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.025"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="false"/>
-        <param name="enable_detection_unspecific_losses" value="false"/>
-        <param name="separate" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.4"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.025"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="true"/>
-        <param name="enable_detection_unspecific_losses" value="true"/>
-        <param name="separate" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathDIAPreScoring">
-</xml>
-  <xml name="autotest_OpenSwathFeatureXMLToTSV">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="short_format" value="true"/>
-      <param name="best_scoring_peptide" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="short_format" value="false"/>
-      <param name="best_scoring_peptide" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="short_format" value="true"/>
-      <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathFileSplitter"/>
-  <xml name="autotest_OpenSwathMzMLFileCacher">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="0.0001"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
-      <param name="out_type" value="sqmass"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
-      <param name="out_type" value="sqmass"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="0.0001"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/>
-      <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="false"/>
-      <param name="full_meta" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathRewriteToFeatureXML">
-</xml>
-  <xml name="autotest_OpenSwathRTNormalizer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
-      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="min_rsq" value="0.95"/>
-      <param name="min_coverage" value="0.6"/>
-      <param name="estimateBestPeptides" value="false"/>
-      <section name="RTNormalization">
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <section name="peptideEstimation">
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
-      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="min_rsq" value="0.95"/>
-      <param name="min_coverage" value="0.6"/>
-      <param name="estimateBestPeptides" value="true"/>
-      <section name="RTNormalization">
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <section name="peptideEstimation">
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="3"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="3"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
-      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="min_rsq" value="0.95"/>
-      <param name="min_coverage" value="0.6"/>
-      <param name="estimateBestPeptides" value="false"/>
-      <section name="RTNormalization">
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <section name="peptideEstimation">
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathWorkflow">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="false"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="false"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
-      <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="cache"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="cacheWorkingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="true"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
-      <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="false"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="550.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
-      <param name="tr_type" value=""/>
-      <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="true"/>
-      <param name="rt_extraction_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.2"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="none"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="true"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
-      <param name="tr_type" value="pqp"/>
-      <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="sqMass"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
-      <param name="tr_type" value="pqp"/>
-      <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="2"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="true"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="2"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="true"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="cache"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="true"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
-      <param name="tr_type" value="pqp"/>
-      <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.6666666666666666"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="true"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PeakPickerHiRes">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_5_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="0.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value=""/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PeakPickerIterative">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerIterative_1_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise_" value="1.0"/>
-        <param name="peak_width" value="0.04"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="sn_bin_count_" value="30"/>
-        <param name="nr_iterations_" value="5"/>
-        <param name="sn_win_len_" value="20.0"/>
-        <param name="check_width_internally" value="false"/>
-        <param name="ms1_only" value="false"/>
-        <param name="clear_meta_data" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerIterative_2_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise_" value="0.0"/>
-        <param name="peak_width" value="0.04"/>
-        <param name="spacing_difference" value="2.5"/>
-        <param name="sn_bin_count_" value="30"/>
-        <param name="nr_iterations_" value="5"/>
-        <param name="sn_win_len_" value="20.0"/>
-        <param name="check_width_internally" value="true"/>
-        <param name="ms1_only" value="false"/>
-        <param name="clear_meta_data" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PeakPickerWavelet">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="3.0"/>
-        <param name="centroid_percentage" value="0.6"/>
-        <param name="peak_width" value="0.2"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="0.5"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="100.0"/>
-          <param name="peak_bound_ms2_level" value="10.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="false"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.12"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="10"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="2.0"/>
-        <param name="centroid_percentage" value="0.8"/>
-        <param name="peak_width" value="0.15"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="1.0"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="200.0"/>
-          <param name="peak_bound_ms2_level" value="50.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="true"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.1"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="100"/>
-            <section name="penalties">
-              <param name="position" value="1.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="3.0"/>
-        <param name="centroid_percentage" value="0.6"/>
-        <param name="peak_width" value="0.2"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="0.5"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="100.0"/>
-          <param name="peak_bound_ms2_level" value="10.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="false"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.12"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="10"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="3.0"/>
-        <param name="centroid_percentage" value="0.6"/>
-        <param name="peak_width" value="0.2"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="0.5"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="100.0"/>
-          <param name="peak_bound_ms2_level" value="10.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="false"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.12"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="10"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PepNovoAdapter">
-</xml>
-  <xml name="autotest_PeptideIndexer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="true"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="0"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_2.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="3"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_3.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="full"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_3.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="semi"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_3.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="remove"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_10_input.idXML"/>
-      <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
-      <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="error"/>
-      <param name="aaa_max" value="3"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="true"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="auto"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="empty.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="error"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="auto"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_14.idXML"/>
-      <param name="fasta" value="PeptideIndexer_2.fasta"/>
-      <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="error"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PercolatorAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.5"/>
-        <param name="trainFDR" value="0.5"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PercolatorAdapter_1.idXML"/>
-      <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms2"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.01"/>
-        <param name="trainFDR" value="0.01"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_osw" value="PercolatorAdapter_2.osw"/>
-      <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <param name="out_type" value="osw"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms1"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.01"/>
-        <param name="trainFDR" value="0.01"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/>
-      <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <param name="out_type" value="osw"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms2"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.01"/>
-        <param name="trainFDR" value="0.01"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/>
-      <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <param name="out_type" value="osw"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="transition"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.5"/>
-        <param name="trainFDR" value="0.5"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PercolatorAdapter_1.idXML"/>
-      <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="idXML"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms2"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PhosphoScoring">
-</xml>
-  <xml name="autotest_PrecursorIonSelector">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="solver" value="GLPK"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
-      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
-      <param name="num_precursors" value="1"/>
-      <param name="load_preprocessing" value="false"/>
-      <param name="store_preprocessing" value="false"/>
-      <param name="simulation" value="true"/>
-      <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <section name="algorithm">
-        <param name="type" value="IPS"/>
-        <param name="max_iteration" value="10"/>
-        <param name="rt_bin_capacity" value="10"/>
-        <param name="step_size" value="1"/>
-        <param name="peptide_min_prob" value="0.2"/>
-        <param name="sequential_spectrum_order" value="false"/>
-        <section name="MIPFormulation">
-          <section name="thresholds">
-            <param name="min_protein_probability" value="0.2"/>
-            <param name="min_protein_id_probability" value="0.95"/>
-            <param name="min_pt_weight" value="0.5"/>
-            <param name="min_mz" value="500.0"/>
-            <param name="max_mz" value="5000.0"/>
-            <param name="min_pred_pep_prob" value="0.5"/>
-            <param name="min_rt_weight" value="0.5"/>
-            <param name="use_peptide_rule" value="true"/>
-            <param name="min_peptide_ids" value="2"/>
-            <param name="min_peptide_probability" value="0.95"/>
-          </section>
-          <section name="combined_ilp">
-            <param name="k1" value="0.2"/>
-            <param name="k2" value="0.2"/>
-            <param name="k3" value="0.4"/>
-            <param name="scale_matching_probs" value="true"/>
-          </section>
-          <section name="feature_based">
-            <param name="no_intensity_normalization" value="false"/>
-            <param name="max_number_precursors_per_feature" value="1"/>
-          </section>
-        </section>
-        <section name="Preprocessing">
-          <param name="precursor_mass_tolerance" value="0.9"/>
-          <param name="precursor_mass_tolerance_unit" value="Da"/>
-          <param name="preprocessed_db_path" value=""/>
-          <param name="preprocessed_db_pred_rt_path" value=""/>
-          <param name="preprocessed_db_pred_dt_path" value=""/>
-          <param name="max_peptides_per_run" value="100000"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="taxonomy" value=""/>
-          <param name="store_peptide_sequences" value="false"/>
-          <section name="rt_settings">
-            <param name="min_rt" value="960.0"/>
-            <param name="max_rt" value="3840.0"/>
-            <param name="rt_step_size" value="30.0"/>
-            <param name="gauss_mean" value="-1.0"/>
-            <param name="gauss_sigma" value="3.0"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="solver" value="GLPK"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
-      <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
-      <param name="num_precursors" value="1"/>
-      <param name="load_preprocessing" value="false"/>
-      <param name="store_preprocessing" value="false"/>
-      <param name="simulation" value="false"/>
-      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <section name="algorithm">
-        <param name="type" value="IPS"/>
-        <param name="max_iteration" value="10"/>
-        <param name="rt_bin_capacity" value="10"/>
-        <param name="step_size" value="1"/>
-        <param name="peptide_min_prob" value="0.2"/>
-        <param name="sequential_spectrum_order" value="false"/>
-        <section name="MIPFormulation">
-          <section name="thresholds">
-            <param name="min_protein_probability" value="0.2"/>
-            <param name="min_protein_id_probability" value="0.95"/>
-            <param name="min_pt_weight" value="0.5"/>
-            <param name="min_mz" value="500.0"/>
-            <param name="max_mz" value="5000.0"/>
-            <param name="min_pred_pep_prob" value="0.5"/>
-            <param name="min_rt_weight" value="0.5"/>
-            <param name="use_peptide_rule" value="true"/>
-            <param name="min_peptide_ids" value="2"/>
-            <param name="min_peptide_probability" value="0.95"/>
-          </section>
-          <section name="combined_ilp">
-            <param name="k1" value="0.2"/>
-            <param name="k2" value="0.2"/>
-            <param name="k3" value="0.4"/>
-            <param name="scale_matching_probs" value="true"/>
-          </section>
-          <section name="feature_based">
-            <param name="no_intensity_normalization" value="false"/>
-            <param name="max_number_precursors_per_feature" value="1"/>
-          </section>
-        </section>
-        <section name="Preprocessing">
-          <param name="precursor_mass_tolerance" value="0.9"/>
-          <param name="precursor_mass_tolerance_unit" value="Da"/>
-          <param name="preprocessed_db_path" value=""/>
-          <param name="preprocessed_db_pred_rt_path" value=""/>
-          <param name="preprocessed_db_pred_dt_path" value=""/>
-          <param name="max_peptides_per_run" value="100000"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="taxonomy" value=""/>
-          <param name="store_peptide_sequences" value="false"/>
-          <section name="rt_settings">
-            <param name="min_rt" value="960.0"/>
-            <param name="max_rt" value="3840.0"/>
-            <param name="rt_step_size" value="30.0"/>
-            <param name="gauss_mean" value="-1.0"/>
-            <param name="gauss_sigma" value="3.0"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PrecursorMassCorrector">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_charge" value="3"/>
-        <param name="intensity_threshold" value="-1.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PrecursorMassCorrector_1_input.mzML"/>
-      <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="precursor_mass_tolerance" value="1.5"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ProteinInference">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinInference_1_input.idXML"/>
-      <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="merge_runs" value="all"/>
-      <param name="annotate_indist_groups" value="true"/>
-      <section name="Merging">
-        <param name="annotate_origin" value="false"/>
-        <param name="allow_disagreeing_settings" value="false"/>
-      </section>
-      <section name="Algorithm">
-        <param name="min_peptides_per_protein" value="1"/>
-        <param name="score_aggregation_method" value="maximum"/>
-        <param name="treat_charge_variants_separately" value="true"/>
-        <param name="treat_modification_variants_separately" value="true"/>
-        <param name="use_shared_peptides" value="false"/>
-        <param name="skip_count_annotation" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ProteinQuantifier">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="median"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="true"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="mean"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="true"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="true"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.idXML"/>
-      <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ProteinResolver">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="fasta" value="ProteinResolver_1_input.fasta"/>
-      <param name="in" value="ProteinResolver_1_input.consensusXML"/>
-      <param name="in_path" value=""/>
-      <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <section name="resolver">
-        <param name="missed_cleavages" value="2"/>
-        <param name="min_length" value="6"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="designer">
-        <param name="experiment" value="ExperimentalSetting"/>
-        <param name="file" value="File"/>
-        <param name="separator" value="tab"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PSMFeatureExtractor">
-</xml>
-  <xml name="autotest_PTModel">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_positive" value="PTModel_1_input_positive.idXML"/>
-      <param name="in_negative" value="PTModel_1_input_negative.idXML"/>
-      <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="c" value="0.5"/>
-      <param name="svm_type" value="C_SVC"/>
-      <param name="nu" value="0.5"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="max_positive_count" value="1000"/>
-      <param name="max_negative_count" value="1000"/>
-      <param name="redundant" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="100.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.1"/>
-        <param name="nu_step_size" value="1.3"/>
-        <param name="nu_stop" value="0.9"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_QCCalculator">
-</xml>
-  <xml name="autotest_QCEmbedder">
-</xml>
-  <xml name="autotest_QCExporter">
-</xml>
-  <xml name="autotest_QCExtractor">
-</xml>
-  <xml name="autotest_QCImporter">
-</xml>
-  <xml name="autotest_QCMerger">
-</xml>
-  <xml name="autotest_QCShrinker">
-</xml>
-  <xml name="autotest_QualityControl">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="QualityControl_1_in.consensusXML"/>
-      <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/>
-      <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
-      <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="in_contaminants" value="QualityControl_1.fasta"/>
-      <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
-      <section name="FragmentMassError">
-        <param name="unit" value="auto"/>
-        <param name="tolerance" value="20.0"/>
-      </section>
-      <section name="MS2_id_rate">
-        <param name="assume_all_target" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_RNADigestor">
-</xml>
-  <xml name="autotest_RNAMassCalculator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_seq" value="&quot;AUCGGC&quot;"/>
-      <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="charge" value="-1 -2"/>
-      <param name="format" value="list"/>
-      <param name="average_mass" value="false"/>
-      <param name="fragment_type" value="full"/>
-      <param name="separator" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_RNPxlSearch">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value="Oxidation (M)"/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="1"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value="GUA"/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="false"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value="Oxidation (M)"/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="1"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value="GUA"/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="true"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="3"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value=""/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="false"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="2"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value=""/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="true"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_RNPxlXICFilter">
-</xml>
-  <xml name="autotest_RTEvaluation">
-</xml>
-  <xml name="autotest_RTModel">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RTModel_1_input.idXML"/>
-      <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.1"/>
-      <param name="kernel_type" value="POLY"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="total_gradient_time" value="3000.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="10.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.3"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.7"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_positive" value="RTModel_2_input_positive.idXML"/>
-      <param name="in_negative" value="RTModel_2_input_negative.idXML"/>
-      <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.5"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="10.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.3"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.7"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RTModel_3_input.idXML"/>
-      <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.001953125"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="1.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="false"/>
-        <param name="number_of_runs" value="1"/>
-        <param name="number_of_partitions" value="5"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="0.001953125"/>
-        <param name="c_step_size" value="2.0"/>
-        <param name="c_stop" value="0.001953125"/>
-        <param name="nu_start" value="0.4"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.4"/>
-        <param name="sigma_start" value="5.0"/>
-        <param name="sigma_step_size" value="1.221055"/>
-        <param name="sigma_stop" value="5.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RTModel_4_input.txt" ftype="txt"/>
-      <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.001953125"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="1.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="false"/>
-        <param name="number_of_runs" value="1"/>
-        <param name="number_of_partitions" value="5"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="0.001953125"/>
-        <param name="c_step_size" value="2.0"/>
-        <param name="c_stop" value="0.001953125"/>
-        <param name="nu_start" value="0.4"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.4"/>
-        <param name="sigma_start" value="5.0"/>
-        <param name="sigma_step_size" value="1.221055"/>
-        <param name="sigma_stop" value="5.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SeedListGenerator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PepXMLFile_test.mzML"/>
-      <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="use_peptide_mass" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMapper_1_output.featureXML"/>
-      <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="use_peptide_mass" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SemanticValidator">
-</xml>
-  <xml name="autotest_SequenceCoverageCalculator">
-</xml>
-  <xml name="autotest_SimpleSearchEngine">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SimpleSearchEngine_1.mzML"/>
-      <param name="database" value="SimpleSearchEngine_1.fasta"/>
-      <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="Search">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="decoys" value="false"/>
-        <section name="precursor">
-          <param name="mass_tolerance" value="5.0"/>
-          <param name="mass_tolerance_unit" value="ppm"/>
-          <param name="min_charge" value="2"/>
-          <param name="max_charge" value="5"/>
-          <param name="isotopes" value="0 1"/>
-        </section>
-        <section name="fragment">
-          <param name="mass_tolerance" value="0.3"/>
-          <param name="mass_tolerance_unit" value="Da"/>
-        </section>
-        <section name="modifications">
-          <param name="fixed" value=""/>
-          <param name="variable" value="Oxidation (M)"/>
-          <param name="variable_max_per_peptide" value="2"/>
-        </section>
-        <section name="annotate">
-          <param name="PSM" value=""/>
-        </section>
-        <section name="peptide">
-          <param name="min_size" value="7"/>
-          <param name="max_size" value="40"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="motif" value=""/>
-        </section>
-        <section name="report">
-          <param name="top_hits" value="1"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SiriusAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_1_input.mzML"/>
-      <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="pubchem"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpecLibCreator">
-</xml>
-  <xml name="autotest_SpecLibSearcher">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpecLibSearcher_1.mzML"/>
-      <param name="lib" value="SpecLibSearcher_1.MSP"/>
-      <output_collection name="out" count="1"/>
-      <param name="compare_function" value="ZhangSimilarityScore"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="3.0"/>
-        <param name="mass_tolerance_unit" value="Da"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="10.0"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="10"/>
-      </section>
-      <section name="filter">
-        <param name="remove_peaks_below_threshold" value="2.01"/>
-        <param name="min_peaks" value="5"/>
-        <param name="max_peaks" value="150"/>
-        <param name="cut_peaks_below" value="1000"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpectraFilterBernNorm">
-</xml>
-  <xml name="autotest_SpectraFilterMarkerMower">
-</xml>
-  <xml name="autotest_SpectraFilterNLargest">
-</xml>
-  <xml name="autotest_SpectraFilterNormalizer">
-</xml>
-  <xml name="autotest_SpectraFilterParentPeakMower">
-</xml>
-  <xml name="autotest_SpectraFilterScaler">
-</xml>
-  <xml name="autotest_SpectraFilterSqrtMower">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-      <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpectraFilterThresholdMower">
-</xml>
-  <xml name="autotest_SpectraFilterWindowMower">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="windowsize" value="50.0"/>
-        <param name="peakcount" value="2"/>
-        <param name="movetype" value="slide"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="windowsize" value="20.0"/>
-        <param name="peakcount" value="4"/>
-        <param name="movetype" value="slide"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpectraMerger">
-</xml>
-  <xml name="autotest_SpectraSTSearchAdapter"/>
-  <xml name="autotest_StaticModification">
-</xml>
-  <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
-</xml>
-  <xml name="autotest_TargetedFileConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="minutes"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="seconds"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/>
-      <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/>
-      <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/>
-      <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="true"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="true"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_output.TraML"/>
-      <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="true"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/>
-      <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_5_output.TraML"/>
-      <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="traml"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TextExporter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_2_input.consensusXML"/>
-      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="true"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="RT_then_MZ"/>
-        <param name="sort_by_maps" value="true"/>
-        <param name="sort_by_size" value="true"/>
-      </section>
-      <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="true"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_5_input.idXML"/>
-      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="true"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="true"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_6_input.featureXML"/>
-      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="true"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_7_input.consensusXML"/>
-      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="RT_then_MZ"/>
-        <param name="sort_by_maps" value="true"/>
-        <param name="sort_by_size" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="true"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_9_input.idXML"/>
-      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="0"/>
-        <param name="add_hit_metavalues" value="0"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TICCalculator">
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="regular"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="streaming"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="streaming"/>
-      <param name="loadData" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="indexed"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="indexed_parallel"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TOFCalibration">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TOFCalibration_1_input.mzML"/>
-      <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
-      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
-      <param name="peak_data" value="false"/>
-      <section name="algorithm">
-        <section name="PeakPicker">
-          <param name="signal_to_noise" value="3.0"/>
-          <param name="centroid_percentage" value="0.6"/>
-          <param name="peak_width" value="0.15"/>
-          <param name="estimate_peak_width" value="false"/>
-          <param name="fwhm_lower_bound_factor" value="0.7"/>
-          <param name="fwhm_upper_bound_factor" value="20.0"/>
-          <section name="optimization">
-            <param name="iterations" value="400"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="left_width" value="1.0"/>
-              <param name="right_width" value="1.0"/>
-              <param name="height" value="1.0"/>
-            </section>
-            <section name="2d">
-              <param name="tolerance_mz" value="2.2"/>
-              <param name="max_peak_distance" value="1.2"/>
-            </section>
-          </section>
-          <section name="thresholds">
-            <param name="peak_bound" value="400.0"/>
-            <param name="peak_bound_ms2_level" value="10.0"/>
-            <param name="correlation" value="0.0"/>
-            <param name="noise_level" value="0.1"/>
-            <param name="search_radius" value="3"/>
-          </section>
-          <section name="wavelet_transform">
-            <param name="spacing" value="0.001"/>
-          </section>
-          <section name="deconvolution">
-            <param name="deconvolution" value="false"/>
-            <param name="asym_threshold" value="0.3"/>
-            <param name="left_width" value="2.0"/>
-            <param name="right_width" value="2.0"/>
-            <param name="scaling" value="0.12"/>
-            <section name="fitting">
-              <param name="fwhm_threshold" value="0.7"/>
-              <param name="eps_abs" value="9.999999747378752e-06"/>
-              <param name="eps_rel" value="9.999999747378752e-06"/>
-              <param name="max_iteration" value="10"/>
-              <section name="penalties">
-                <param name="position" value="0.0"/>
-                <param name="height" value="1.0"/>
-                <param name="left_width" value="0.0"/>
-                <param name="right_width" value="0.0"/>
-              </section>
-            </section>
-          </section>
-          <section name="SignalToNoiseEstimationParameter">
-            <param name="max_intensity" value="-1"/>
-            <param name="auto_max_stdev_factor" value="3.0"/>
-            <param name="auto_max_percentile" value="95"/>
-            <param name="auto_mode" value="0"/>
-            <param name="win_len" value="200.0"/>
-            <param name="bin_count" value="30"/>
-            <param name="stdev_mp" value="3.0"/>
-            <param name="min_required_elements" value="10"/>
-            <param name="noise_for_empty_window" value="1e+20"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TOFCalibration_2_input.mzML"/>
-      <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
-      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
-      <param name="peak_data" value="true"/>
-      <section name="algorithm">
-        <section name="PeakPicker">
-          <param name="signal_to_noise" value="3.0"/>
-          <param name="centroid_percentage" value="0.6"/>
-          <param name="peak_width" value="0.15"/>
-          <param name="estimate_peak_width" value="false"/>
-          <param name="fwhm_lower_bound_factor" value="0.7"/>
-          <param name="fwhm_upper_bound_factor" value="20.0"/>
-          <section name="optimization">
-            <param name="iterations" value="400"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="left_width" value="1.0"/>
-              <param name="right_width" value="1.0"/>
-              <param name="height" value="1.0"/>
-            </section>
-            <section name="2d">
-              <param name="tolerance_mz" value="2.2"/>
-              <param name="max_peak_distance" value="1.2"/>
-            </section>
-          </section>
-          <section name="thresholds">
-            <param name="peak_bound" value="400.0"/>
-            <param name="peak_bound_ms2_level" value="10.0"/>
-            <param name="correlation" value="0.0"/>
-            <param name="noise_level" value="0.1"/>
-            <param name="search_radius" value="3"/>
-          </section>
-          <section name="wavelet_transform">
-            <param name="spacing" value="0.001"/>
-          </section>
-          <section name="deconvolution">
-            <param name="deconvolution" value="false"/>
-            <param name="asym_threshold" value="0.3"/>
-            <param name="left_width" value="2.0"/>
-            <param name="right_width" value="2.0"/>
-            <param name="scaling" value="0.12"/>
-            <section name="fitting">
-              <param name="fwhm_threshold" value="0.7"/>
-              <param name="eps_abs" value="9.999999747378752e-06"/>
-              <param name="eps_rel" value="9.999999747378752e-06"/>
-              <param name="max_iteration" value="10"/>
-              <section name="penalties">
-                <param name="position" value="0.0"/>
-                <param name="height" value="1.0"/>
-                <param name="left_width" value="0.0"/>
-                <param name="right_width" value="0.0"/>
-              </section>
-            </section>
-          </section>
-          <section name="SignalToNoiseEstimationParameter">
-            <param name="max_intensity" value="-1"/>
-            <param name="auto_max_stdev_factor" value="3.0"/>
-            <param name="auto_max_percentile" value="95"/>
-            <param name="auto_mode" value="0"/>
-            <param name="win_len" value="200.0"/>
-            <param name="bin_count" value="30"/>
-            <param name="stdev_mp" value="3.0"/>
-            <param name="min_required_elements" value="10"/>
-            <param name="noise_for_empty_window" value="1e+20"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TransformationEvaluation">
-</xml>
-  <xml name="autotest_XFDR">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in1.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in1.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="true"/>
-      <param name="no_qvalues" value="true"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="0.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-3.0"/>
-      <param name="maxborder" value="3.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in3.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-3.0"/>
-      <param name="maxborder" value="3.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in4.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="true"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="0.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_XMLValidator">
-</xml>
-  <xml name="autotest_XTandemAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
-      <param name="ignore_adapter_param" value="false"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="max_precursor_charge" value="0"/>
-      <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="minimum_fragment_mz" value="150.0"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="semi_cleavage" value="false"/>
-      <param name="output_results" value="all"/>
-      <param name="max_valid_expect" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
-      <param name="ignore_adapter_param" value="false"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="max_precursor_charge" value="0"/>
-      <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="minimum_fragment_mz" value="150.0"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="semi_cleavage" value="false"/>
-      <param name="output_results" value="valid"/>
-      <param name="max_valid_expect" value="1e-14"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteinslong.fasta"/>
-      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
-      <param name="ignore_adapter_param" value="false"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="max_precursor_charge" value="0"/>
-      <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="minimum_fragment_mz" value="150.0"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="semi_cleavage" value="false"/>
-      <param name="output_results" value="all"/>
-      <param name="max_valid_expect" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-<xml name="autotest_InspectAdapter"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_RTPredict"/><xml name="autotest_PTPredict"/><xml name="autotest_IDDecoyProbability"/></macros>
--- a/macros_test.xml	Mon Dec 14 16:53:26 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,553 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<macros>
-
-<!-- a copy of a FileConverter test without the advanced options used
-     in order to check if this works (all other tests enable advanced) -->
-<xml name="manutest_FileConverter">
-<test expect_num_outputs="1">
-  <param name="in" value="FileConverter_1_input.mzData"/>
-  <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-  <param name="out_type" value="mzML"/>
-</test>
-</xml>
-<!-- tests contributed by the galaxyproteomics community -->
-<xml name="manutest_ClusterMassTracesByPrecursor">
-  <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
-  </test>
-</xml>
-<xml name="manutest_ClusterMassTraces">
-  <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
-  </test>
-</xml>
-<xml name="manutest_CVInspector">
-  <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 -->
-  <test expect_num_outputs="1">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
-    <param name="cv_names" value="XLMOD"/>
-    <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
-    <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
-    <output name="html" ftype="html" value="CVInspector.html"/>
-  </test>
-</xml>
-<xml name="manutest_DeMeanderize">
-  <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
-	<output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
-  </test>
-</xml>
-<xml name="manutest_Digestor">
-  <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="random.fa"/>
-    <output name="out" ftype="fasta" value="Digestor.fasta"/>
-    <param name="out_type" value="fasta"/>
-  </test>
-</xml>
-<xml name="manutest_EICExtractor">
-  <test expect_num_outputs="1"><!-- just using some random test data -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="spectra.mzML"/>
-    <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
-    <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
-  </test>
-</xml>
-<xml name="manutest_ERPairFinder">
-  <!-- TODO -->
-</xml>
-<xml name="manutest_FeatureFinderIsotopeWavelet">
-  <test expect_num_outputs="1"><!--just use the input of another FeatureFinder -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
-    <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_FFEval">
-  <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
-    <output name="out" value="FFEval.featureXML" compare="sim_size"/>
-	<output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
-  </test>
-</xml>
-<xml name="manutest_IDExtractor">
-  <test expect_num_outputs="1"><!--  -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="best_hits" value="true"/>
-    <param name="number_of_peptides" value="1"/>
-    <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
-  </test>
-</xml>
-<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
-<xml name="manutest_IDRipper">
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="IDRipper_1_input.idXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output_collection name="out_path" count="2">
-    <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
-    <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
-  </output_collection>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="IDRipper_2_input.idXML"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output_collection name="out_path" count="2">
-    <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/>
-    <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/>
-  </output_collection>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="IDRipper_3_output.idXML"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output_collection name="out_path" count="2">
-    <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/>
-    <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/>
-  </output_collection>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
-</xml>
-<xml name="manutest_LabeledEval">
-  <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
-    <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/>
-    <output name="stdout" value="LabeledEval.txt" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_MapStatistics">
-  <test expect_num_outputs="1"><!-- test with a featureXML input  -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
-    <output name="out" ftype="txt" value="MapStatistics.txt"/>
-  </test>
-  <test expect_num_outputs="1"><!-- test with a consensusxml input -->
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
-    <output name="out" ftype="txt" value="MapStatistics2.txt"/>
-  </test>
-</xml>
-<xml name="manutest_MetaboliteSpectralMatcher">
-    <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="database" value="MetaboliteSpectralDB.mzML"/>
-    <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
-  </test>
-</xml>
-<xml name="manutest_MRMPairFinder">
-  <!-- TODO no idea about a useful input for pair_in -->
-</xml>
-<xml name="manutest_MSSimulator">
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-    <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/>
-  </test>
-</xml>
-<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
-<xml name="manutest_MzMLSplitter">
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="2"/>
-  <param name="size" value="0"/>
-  <param name="unit" value="MB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="1"/>
-  <param name="size" value="40"/>
-  <param name="unit" value="KB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-</xml>
-<xml name="manutest_OpenSwathDIAPreScoring">
-  <!-- data from a test that included all the needed test files -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-    <output_collection name="output_files" count="1">
-      <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-
-  <!-- test with two inputs (actually the same file .. symlinked) -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
-    <output_collection name="output_files" count="2">
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-</xml>
-<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
-<xml name="manutest_OpenSwathFileSplitter">
-  <test expect_num_outputs="3">
-    <conditional name="adv_opts_cond">
-      <param name="adv_opts_selector" value="advanced"/>
-      <param name="force" value="false"/>
-      <param name="test" value="true"/>
-    </conditional>
-    <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
-    <output_collection name="outputDirectory" count="6">
-      <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
-      <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
-    </output_collection>
-    <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
-    <output name="ctd_out" ftype="xml">
-      <assert_contents>
-        <is_valid_xml/>
-      </assert_contents>
-    </output>
-  </test>
-</xml>
-<xml name="manutest_OpenSwathRewriteToFeatureXML">
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
-  </test>
-</xml>
-<xml name="manutest_PepNovoAdapter">
-  <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection
-             unclear https://github.com/OpenMS/OpenMS/issues/4719)-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-</xml>
-<xml name="manutest_PhosphoScoring">
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
-    <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
-  </test>
-</xml>
-<!-- TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 -->
-<xml name="manutest_PSMFeatureExtractor">
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|skip_db_check" value="true"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
-  </test>
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|skip_db_check" value="true"/>
-    <param name="out_type" value="mzid"/>
-    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
-  </test>
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
-  </test>
-</xml>
-<xml name="manutest_QCCalculator">
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
-    <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
-    <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
-    <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
-    <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
-    <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
-  </test>
-</xml>
-<xml name="manutest_QCEmbedder">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCExporter">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCExtractor">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCImporter">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCMerger">
-  <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
-    <output name="out" ftype="qcml" value="QCMerger.qcML"/>
-  </test>
-</xml>
-<xml name="manutest_QCShrinker">
-  <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input  -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
-    <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
-  </test>
-</xml>
-<xml name="manutest_RNADigestor">
-  <test expect_num_outputs="1"><!--random RNAsequence input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="random_RNA.fa"/>
-    <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
-  </test>
-</xml>
-<xml name="manutest_RNPxlXICFilter">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
-  </test>
-</xml>
-<xml name="manutest_RTEvaluation">
-  <!-- just chosen an arbitrary input and autgenerated output-->
-  <test expect_num_outputs="1">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
-    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
-  </test>
-</xml>
-<xml name="manutest_SemanticValidator">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
-    <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
-       <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents>
-    </output>
-  </test>
-</xml>
-<xml name="manutest_SequenceCoverageCalculator">
-  <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
-    <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
-    <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpecLibCreator">
-  <!--TODO could not find test data -->
-</xml>
-<xml name="manutest_SpectraFilterBernNorm">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterMarkerMower">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterNLargest">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterNormalizer">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterParentPeakMower">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterScaler">
-  <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterThresholdMower">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraMerger">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
-    <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer">
-<!-- -TODO model_output_file creates multiple files-->
-</xml>
-<xml name="manutest_TransformationEvaluation">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/>
-  </test>
-</xml>
-<xml name="manutest_XMLValidator">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
-       <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
-    </output>
-  </test>
-</xml>
-<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
--- a/readme.md	Mon Dec 14 16:53:26 2020 +0000
+++ b/readme.md	Thu Dec 01 19:16:56 2022 +0000
@@ -74,10 +74,15 @@

 Preprocessing:

-- For each input / output data set parameter a directory is crated (named by
-  the parameter)
 - For input data set parameters the links to the actual location of the data
-  sets are created
+  sets are created, the link names are `element_identifier`.`EXT`, where `EXT`
+  is an extension that is known by OpenMS
+- In order to avoid name collisions for the created links each is placed in a
+  unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name
+  of the parameter and `DATASET_ID` is the id of the Galaxy dataset
+- the same happens for output parameters that are in 1:1 correspondence with
+  an input parameter
+

 Main:
--- a/test-data.sh	Mon Dec 14 16:53:26 2020 +0000
+++ b/test-data.sh	Thu Dec 01 19:16:56 2022 +0000
@@ -1,22 +1,25 @@
 #!/usr/bin/env bash

-VERSION=2.6
-FILETYPES="filetypes.txt"
-CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2"
+VERSION=2.8
+FILETYPES="aux/filetypes.txt"
+CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2"

 # import the magic
 . ./generate-foo.sh

 # install conda
 if [ -z "$tmp" ]; then
-	tmp=$(mktemp -d)
-	created="yes"
+    tmp=$(mktemp -d)
+    created="yes"
 fi

 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"
 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
-export OPENMSENV="$tmp/OpenMS$VERSION-env"
-export CTDCONVERTER="$tmp/CTDConverter"
+export OPENMSENV="OpenMS$VERSION-env"
+
+if [ -z "$CTDCONVERTER" ]; then
+    export CTDCONVERTER="$tmp/CTDConverter"
+fi

 if [[ -z "$1" ]]; then
 	autotests="/dev/null"
@@ -25,11 +28,11 @@
 fi

 if type conda > /dev/null; then
-	true
+    true
 else
-	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-	bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
-	source "$tmp/miniconda/bin/activate"
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
+    source "$tmp/miniconda/bin/activate"
 fi
 eval "$(conda shell.bash hook)"

@@ -42,24 +45,27 @@

 echo "Clone OpenMS $VERSION sources"
 if [[ ! -d $OPENMSGIT ]]; then
-	git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
-	cd $OPENMSGIT
-	git submodule init
-	git submodule update
-	cd -
+    # TODO >2.8 reenable original release branch .. also in else branch
+    # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917
+    # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
+    git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT
+    cd $OPENMSGIT
+    git submodule init
+    git submodule update
+    cd -
 else
-	cd $OPENMSGIT
-	git pull origin release/$VERSION.0
-	cd -
+    cd $OPENMSGIT
+    git pull origin release/$VERSION.0-plus
+    cd -
 fi

 echo "Create OpenMS $VERSION conda env"
 # TODO currently add lxml (needed by CTDConverter)
 # TODO for some reason a to recent openjdk is used
 if conda env list | grep "$OPENMSENV"; then
-	true
+    true
 else
-	conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml
+    conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml
 # chmod -R u-w $OPENMSENV
 fi
 ###############################################################################
@@ -69,10 +75,10 @@
 echo "Download OpenMS $VERSION package $CONDAPKG"

 if [[ ! -d $OPENMSPKG ]]; then
-	mkdir $OPENMSPKG
-	wget -q -P $OPENMSPKG/ "$CONDAPKG"
-	tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
-	rm $OPENMSPKG/"$(basename $CONDAPKG)"
+    mkdir $OPENMSPKG
+    wget -q -P $OPENMSPKG/ "$CONDAPKG"
+    tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
+    rm $OPENMSPKG/"$(basename $CONDAPKG)"
 fi

 ###############################################################################
@@ -81,40 +87,46 @@
 ###############################################################################
 echo "Clone CTDConverter"
 if [[ ! -d $CTDCONVERTER ]]; then
-	#git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
-	git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
+    #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
+    git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
 else
-	cd $CTDCONVERTER
-	git pull origin topic/cdata
-	cd -
+    cd $CTDCONVERTER
+    git pull origin topic/fix-selects2
+    cd -
 fi
+conda activate $OPENMSENV
+cd $CTDCONVERTER
+python -m pip install . --no-deps
+cd -
+conda deactivate

-###############################################################################
-## copy all the test data files to test-data
-## most of it (outputs) will be overwritten later, but its needed for
-## prepare_test_data
-###############################################################################
+
+# ###############################################################################
+# ## copy all the test data files to test-data
+# ## most of it (outputs) will be overwritten later, but its needed for
+# ## prepare_test_data
+# ###############################################################################
 echo "Get test data"
-find test-data -type f,l,d ! -name "*fa"  ! -name "*loc" -delete
+find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete

 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
-if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then
-	wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
-	mv MetaboliteSpectralDB.mzML test-data/
+if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then
+    wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
+    mv MetaboliteSpectralDB.mzML test-data/
 fi
 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv

 if [ ! -d test-data/pepnovo_models/ ]; then
-	mkdir -p /tmp/pepnovo
-	wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
-	unzip PepNovo.20120423.zip -d /tmp/pepnovo/
-	mv /tmp/pepnovo/Models test-data/pepnovo_models/
-	rm PepNovo.20120423.zip
-	rm -rf /tmp/pepnovo
+    mkdir -p /tmp/pepnovo
+    wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
+    unzip PepNovo.20120423.zip -d /tmp/pepnovo/
+    mv /tmp/pepnovo/Models test-data/pepnovo_models/
+    rm PepNovo.20120423.zip
+    rm -rf /tmp/pepnovo
 fi
 ###############################################################################
 ## generate ctd files using the binaries in the conda package
@@ -124,17 +136,13 @@
 rm -rf ctd
 mkdir -p ctd

-# TODO because of https://github.com/OpenMS/OpenMS/issues/4641
-# this needs to be done from within test-data
-cd test-data
 for i in $OPENMSPKG/bin/*
 do
-	b=$(basename $i)
-	echo $b
-	$b -write_ctd ../ctd/
-	sed -i -e 's/²/^2/' ../ctd/$b.ctd
+    b=$(basename $i)
+    echo $b
+    $b -write_ctd ctd/
+    sed -i -e 's/²/^2/' ctd/$b.ctd
 done
-cd -
 ###############################################################################
 ## fix ini files: OpenMS test data contains ini files with outdated ini files.
 ## e.g. variables might be in different nodes, outdated variables present, new
@@ -146,17 +154,17 @@
 echo "Update test INI files"
 for ini in test-data/*ini
 do
-	tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
-	bin=$(which $tool)
-	if [[ -z $bin ]]; then
+    tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
+    bin=$(which $tool)
+    if [[ -z $bin ]]; then
           >&2 echo "missing binary to convert $ini"
-		  continue
-	fi
-	cp $ini $ini.backup
-	$bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
-	if [[ "$?" -ne "0" ]]; then
-		>&2 echo "could not convert $ini"
-	fi
+          continue
+    fi
+    cp $ini $ini.backup
+    $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
+    if [[ "$?" -ne "0" ]]; then
+        >&2 echo "could not convert $ini"
+    fi
 done

 ###############################################################################
@@ -185,17 +193,17 @@

 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh

-# prepare_test_data > tmp_test_data.sh
-# # remove calls not needed for the tools listed in any .list file
-# echo LIST $LIST
-# if [ ! -z "$LIST" ]; then
-# 	REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
-# else
-# 	REX=".*"
-# fi
-# echo REX $REX
-# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
-# rm tmp_test_data.sh
+## prepare_test_data > tmp_test_data.sh
+## # remove calls not needed for the tools listed in any .list file
+## echo LIST $LIST
+## if [ ! -z "$LIST" ]; then
+##     REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
+## else
+##     REX=".*"
+## fi
+## echo REX $REX
+## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
+## rm tmp_test_data.sh

 echo "Execute test shell script"
 chmod u+x prepare_test_data.sh
@@ -204,14 +212,13 @@
 cd - || exit


-###############################################################################
-## create/update test data for the manually generated tests
-## - run convert once with the manual tests only and
-## - update test-data (needs to run 2x)
-###############################################################################
+# ###############################################################################
+# ## create/update test data for the manually generated tests
+# ## - run convert once with the manual tests only and
+# ## - update test-data (needs to run 2x)
+# ###############################################################################
 echo "Execute test shell script for manually curated tests"
 chmod u+x prepare_test_data_manual.sh
-
 cd ./test-data || exit
 ../prepare_test_data_manual.sh
 cd - || exit
@@ -220,22 +227,28 @@
 ###############################################################################
 ## auto generate tests
 ###############################################################################
+
 echo "Write test macros to $autotests"
 echo "<macros>" > "$autotests"
-for i in $(ls *xml |grep -v macros)
+
+for i in $(ls ctd/*ctd)
 do
-	b=$(basename "$i" .xml)
-	get_tests2 "$b" >> "$autotests"
+    b=$(basename "$i" .ctd)
+    get_tests2 "$b" >> "$autotests"
 done
 echo "</macros>" >> "$autotests"

-echo "Create test data links"
-link_tmp_files
+# echo "Create test data links"
+# Breaks DecoyDatabase
+# link_tmp_files

 # tests for tools using output_prefix parameters can not be auto generated
 # hence we output the tests for manual curation in macros_test.xml
 # and remove them from the autotests
-# -> OpenSwathFileSplitter IDRipper MzMLSplitter
+# -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator
+# TODO reevaluate in >2.8
+# - https://github.com/OpenMS/OpenMS/pull/5873
+# - https://github.com/OpenMS/OpenMS/pull/5912
 #
 # Furthermore we remove tests for tools without binaries in conda
 # -> MSFragger MaRaClusterAdapter NovorAdapter
@@ -243,23 +256,23 @@
 # not able to specify composite test data
 # -> SpectraSTSearchAdapter
 if [[ ! -z "$1" ]]; then
-	echo "" > macros_discarded_auto.xml
-	for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
-	do
-		echo "<xml name=\"manutest_$i\">" >>  macros_discarded_auto.xml
-		xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >>  macros_discarded_auto.xml
-		echo "</xml>"  >>  macros_discarded_auto.xml
-		xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
-		mv tmp macros_autotest.xml
-	done
-	>&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
+    echo "" > macros_discarded_auto.xml
+    for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
+    do
+        echo "<xml name=\"manutest_$i\">" >>  macros_discarded_auto.xml
+        xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >>  macros_discarded_auto.xml
+        echo "</xml>"  >>  macros_discarded_auto.xml
+        xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
+        mv tmp macros_autotest.xml
+    done
+    >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
 fi
 conda deactivate

 ## remove broken symlinks in test-data
 find test-data/ -xtype l -delete

-# if [ ! -z "$created" ]; then
-# 	echo "Removing temporary directory"
-# 	rm -rf "$tmp"
-# fi
+if [ ! -z "$created" ]; then
+    echo "Removing temporary directory"
+    rm -rf "$tmp"
+fi
--- a/test-data/spectrast.log	Mon Dec 14 16:53:26 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML
-GENERAL: File offset size is 8 bytes. Big library supported.
-GENERAL: Pointer size is 8 bytes.
-MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z
-MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ;
-PERFORMANCE: Total Run Time = 0 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0 seconds..
-
-END: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML
-==========
-START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML
-GENERAL: File offset size is 8 bytes. Big library supported.
-GENERAL: Pointer size is 8 bytes.
-MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z
-MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ;
-PERFORMANCE: Total Run Time = 1 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0.333333 seconds..
-
-END: (Sun Dec 13 17:22:44 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML
-==========