annotate IDFileConverter.xml @ 16:5e9c35b8d194 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--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: [File Converter]-->
<tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Converts identification engine file formats</description>
  <macros>
    <token name="@EXECUTABLE@">IDFileConverter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&
#if $mz_file:
  mkdir mz_file &&
  cp '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${out_type}'
#if $mz_file:
  -mz_file
  'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)'
#end if

## Postprocessing
&& mv 'out/output.${out_type}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml" label="Input file or directory containing the data to convert" help="This may be:. - a single file in OpenMS database format (.oms),. - a single file in a multi-purpose XML format (.idXML, .mzid, .pepXML, .protXML),. - a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),. - a single file in fasta format (can only be used to generate a theoretical mzML),. - a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),. - for Sequest results, a directory containing .out files..  select fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml data sets(s)"/>
    <param argument="-out_type" type="select" label="Output file type (default: determined from file extension)" help="">
      <option value="fasta">fasta</option>
      <option value="idXML">idxml</option>
      <option value="mzML">mzml</option>
      <option value="mzid">mzid</option>
      <option value="oms">sqlite (oms)</option>
      <option value="pepXML">pepxml</option>
      <option value="xquest.xml">xquest.xml</option>
      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
      <expand macro="list_string_san" name="out_type"/>
    </param>
    <param argument="-mz_file" type="data" format="mzdata,mzml,mzxml" optional="true" label="[pepXML, Sequest, Mascot, X" help="Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file select mzdata,mzml,mzxml data sets(s)"/>
    <param argument="-mz_name" type="text" optional="true" value="" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="Only necessary if different from 'mz_file'">
      <expand macro="list_string_san" name="mz_name"/>
    </param>
    <param argument="-peptideprophet_analyzed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="By default a 'raw' pepXML is produced that contains only search engine results"/>
    <param argument="-score_type" type="select" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
      <option value="qvalue" selected="true">qvalue</option>
      <option value="PEP">PEP</option>
      <option value="score">score</option>
      <expand macro="list_string_san" name="score_type"/>
    </param>
    <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false">
      <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
        <option value="none" selected="true">none</option>
        <option value="coarse">coarse</option>
        <option value="fine">fine</option>
        <expand macro="list_string_san" name="isotope_model"/>
      </param>
      <param name="max_isotope" argument="-fasta_to_mzml:max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/>
      <param name="max_isotope_probability" argument="-fasta_to_mzml:max_isotope_probability" type="float" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/>
      <param name="add_metainfo" argument="-fasta_to_mzml:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
      <param name="add_losses" argument="-fasta_to_mzml:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
      <param name="sort_by_position" argument="-fasta_to_mzml:sort_by_position" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Sort output by position" help=""/>
      <param name="add_precursor_peaks" argument="-fasta_to_mzml:add_precursor_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds peaks of the unfragmented precursor ion to the spectrum" help=""/>
      <param name="add_all_precursor_charges" argument="-fasta_to_mzml:add_all_precursor_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds precursor peaks with all charges in the given range" help=""/>
      <param name="add_abundant_immonium_ions" argument="-fasta_to_mzml:add_abundant_immonium_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)" help=""/>
      <param name="add_first_prefix_ion" argument="-fasta_to_mzml:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
      <param name="add_y_ions" argument="-fasta_to_mzml:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of y-ions to the spectrum" help=""/>
      <param name="add_b_ions" argument="-fasta_to_mzml:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of b-ions to the spectrum" help=""/>
      <param name="add_a_ions" argument="-fasta_to_mzml:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
      <param name="add_c_ions" argument="-fasta_to_mzml:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
      <param name="add_x_ions" argument="-fasta_to_mzml:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of  x-ions to the spectrum" help=""/>
      <param name="add_z_ions" argument="-fasta_to_mzml:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
      <param name="y_intensity" argument="-fasta_to_mzml:y_intensity" type="float" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/>
      <param name="b_intensity" argument="-fasta_to_mzml:b_intensity" type="float" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/>
      <param name="a_intensity" argument="-fasta_to_mzml:a_intensity" type="float" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/>
      <param name="c_intensity" argument="-fasta_to_mzml:c_intensity" type="float" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/>
      <param name="x_intensity" argument="-fasta_to_mzml:x_intensity" type="float" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/>
      <param name="z_intensity" argument="-fasta_to_mzml:z_intensity" type="float" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/>
      <param name="relative_loss_intensity" argument="-fasta_to_mzml:relative_loss_intensity" type="float" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
      <param name="precursor_intensity" argument="-fasta_to_mzml:precursor_intensity" type="float" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/>
      <param name="precursor_H2O_intensity" argument="-fasta_to_mzml:precursor_H2O_intensity" type="float" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
      <param name="precursor_NH3_intensity" argument="-fasta_to_mzml:precursor_NH3_intensity" type="float" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
      <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" label="Enzym used to digest the fasta proteins" help="">
        <option value="Trypsin" selected="true">Trypsin</option>
        <option value="Arg-C">Arg-C</option>
        <option value="no cleavage">no cleavage</option>
        <option value="unspecific cleavage">unspecific cleavage</option>
        <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
        <option value="Glu-C+P">Glu-C+P</option>
        <option value="PepsinA + P">PepsinA + P</option>
        <option value="cyanogen-bromide">cyanogen-bromide</option>
        <option value="Clostripain/P">Clostripain/P</option>
        <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
        <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
        <option value="Alpha-lytic protease">Alpha-lytic protease</option>
        <option value="2-iodobenzoate">2-iodobenzoate</option>
        <option value="iodosobenzoate">iodosobenzoate</option>
        <option value="staphylococcal protease/D">staphylococcal protease/D</option>
        <option value="Trypsin/P">Trypsin/P</option>
        <option value="V8-DE">V8-DE</option>
        <option value="Arg-C/P">Arg-C/P</option>
        <option value="Asp-N">Asp-N</option>
        <option value="Asp-N/B">Asp-N/B</option>
        <option value="Asp-N_ambic">Asp-N_ambic</option>
        <option value="Chymotrypsin">Chymotrypsin</option>
        <option value="Chymotrypsin/P">Chymotrypsin/P</option>
        <option value="CNBr">CNBr</option>
        <option value="Formic_acid">Formic_acid</option>
        <option value="Lys-C">Lys-C</option>
        <option value="Lys-N">Lys-N</option>
        <option value="Lys-C/P">Lys-C/P</option>
        <option value="PepsinA">PepsinA</option>
        <option value="TrypChymo">TrypChymo</option>
        <option value="V8-E">V8-E</option>
        <option value="leukocyte elastase">leukocyte elastase</option>
        <option value="proline endopeptidase">proline endopeptidase</option>
        <expand macro="list_string_san" name="enzyme"/>
      </param>
      <param name="missed_cleavages" argument="-fasta_to_mzml:missed_cleavages" type="integer" value="0" label="Number of allowed missed cleavages while digesting the fasta proteins" help=""/>
      <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" value="1" label="Minimum charge" help=""/>
      <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" value="1" label="Maximum charge" help=""/>
      <param name="precursor_charge" argument="-fasta_to_mzml:precursor_charge" type="integer" value="0" label="Manually set precursor charge" help="(default: 0, meaning max_charge + 1 will be used as precursor charge)"/>
    </section>
    <expand macro="adv_opts_macro">
      <param argument="-ignore_proteins_per_peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[Sequest only] Workaround to deal with .out files that contain" help="e.g. &quot;+1&quot; in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
      <param argument="-scan_regex" type="text" optional="true" value="" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="See documentation for details">
        <expand macro="list_string_san" name="scan_regex"/>
      </param>
      <param argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectra_data' in protein identifications if 'mz_file' is given and 'spectrum_reference's are added/updated" help="Use only if you are sure it is absolutely the same 'mz_file' as used for identification"/>
      <param argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectrum_reference' in peptide identifications if 'mz_file' is given and a 'spectrum_reference' is already present" help=""/>
      <param argument="-add_ionmatch_annotation" type="float" value="0.0" label="[+mz_file only] Annotate the identifications with ion matches from spectra in 'mz_file' using the given tolerance (in Da)" help="This will take quite some time"/>
      <param argument="-concatenate_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[FASTA output only] Will concatenate the top peptide hits to one peptide sequence, rather than write a new peptide for each hit" help=""/>
      <param argument="-number_of_hits" type="integer" value="1" label="[FASTA output only] Controls how many peptide hits will be exported" help="A value of 0 or less exports all hits"/>
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="fasta">
      <change_format>
        <when input="out_type" value="idXML" format="idxml"/>
        <when input="out_type" value="mzML" format="mzml"/>
        <when input="out_type" value="mzid" format="mzid"/>
        <when input="out_type" value="oms" format="sqlite"/>
        <when input="out_type" value="pepXML" format="pepxml"/>
        <when input="out_type" value="xquest.xml" format="xquest.xml"/>
      </change_format>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_IDFileConverter_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
      <output name="out" value="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="PepXMLFile_test.pepxml"/>
      <output name="out" value="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_3_input.protXML"/>
      <output name="out" value="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_5 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
      <output name="out" value="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_6 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_6_input1.pepXML"/>
      <output name="out" value="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_7 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_7_input1.xml"/>
      <output name="out" value="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_8 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_8_input.mzid"/>
      <output name="out" value="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_9 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_9_input.idXML"/>
      <output name="out" value="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_10 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_10_input.pepXML"/>
      <output name="out" value="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_11 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
      <output name="out" value="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_12 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" value="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_13 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" value="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_14 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" value="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_15 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
      <output name="out" value="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_16 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_16_input.pepXML"/>
      <output name="out" value="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_17 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_17_input.idXML"/>
      <output name="out" value="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_18 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_18_input.idXML"/>
      <output name="out" value="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_19 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_19_input.idXML"/>
      <output name="out" value="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_20 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_20_input.idXML"/>
      <output name="out" value="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_21 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_21_input.idXML"/>
      <output name="out" value="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_22 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
      <output name="out" value="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_23 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_23_input.mzid"/>
      <output name="out" value="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_24 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_24_input.pep.xml"/>
      <output name="out" value="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_25 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_25_input.idXML"/>
      <output name="out" value="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_26 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_26_input.mzid"/>
      <output name="out" value="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_27 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" value="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_28 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" value="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_29 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" value="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_30 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" value="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_31 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_31_input.mzid"/>
      <output name="out" value="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_32 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_32_input.FASTA"/>
      <output name="out" value="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/>
      <param name="out_type" value="mzML"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_33 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_32_input.FASTA"/>
      <output name="out" value="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/>
      <param name="out_type" value="mzML"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="1"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_34_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_34_input.idXML"/>
      <output name="out" value="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
      <param name="out_type" value="oms"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_34_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <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"/>
      </section>
      <param name="in" value="IDFileConverter_34_output1.oms"/>
      <output name="out" value="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" 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"/>
      <section name="fasta_to_mzml">
        <param name="isotope_model" value="none"/>
        <param name="max_isotope" value="2"/>
        <param name="max_isotope_probability" value="0.05"/>
        <param name="add_metainfo" value="false"/>
        <param name="add_losses" value="false"/>
        <param name="sort_by_position" value="true"/>
        <param name="add_precursor_peaks" value="false"/>
        <param name="add_all_precursor_charges" value="false"/>
        <param name="add_abundant_immonium_ions" value="false"/>
        <param name="add_first_prefix_ion" value="false"/>
        <param name="add_y_ions" value="true"/>
        <param name="add_b_ions" value="true"/>
        <param name="add_a_ions" value="false"/>
        <param name="add_c_ions" value="false"/>
        <param name="add_x_ions" value="false"/>
        <param name="add_z_ions" value="false"/>
        <param name="y_intensity" value="1.0"/>
        <param name="b_intensity" value="1.0"/>
        <param name="a_intensity" value="1.0"/>
        <param name="c_intensity" value="1.0"/>
        <param name="x_intensity" value="1.0"/>
        <param name="z_intensity" value="1.0"/>
        <param name="relative_loss_intensity" value="0.1"/>
        <param name="precursor_intensity" value="1.0"/>
        <param name="precursor_H2O_intensity" value="1.0"/>
        <param name="precursor_NH3_intensity" value="1.0"/>
        <param name="enzyme" value="Trypsin"/>
        <param name="missed_cleavages" value="0"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="precursor_charge" 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>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[Converts identification engine file formats.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDFileConverter.html]]></help>
  <expand macro="references"/>
</tool>