diff Epifany.xml @ 4:f3096a586de8 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- a/Epifany.xml	Fri Nov 06 19:40:12 2020 +0000
+++ b/Epifany.xml	Thu Dec 01 19:13:55 2022 +0000
@@ -1,13 +1,11 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Runs a Bayesian protein inference.</description>
   <macros>
     <token name="@EXECUTABLE@">Epifany</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,8 +14,13 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir in_cond.in &&
+#if $in_cond.in_select == "no"
+mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
+${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+#end if
 #if $exp_design:
   mkdir exp_design &&
   ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' &&
@@ -31,7 +34,11 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+#if $in_cond.in_select == "no"
+${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
+#end if
 #if $exp_design:
   -exp_design
   'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)'
@@ -49,21 +56,32 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
-    <param name="exp_design" argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/>
-    <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help="">
+    <conditional name="in_cond">
+      <param name="in_select" type="select" label="Run tool in batch mode for -in">
+        <option value="no">No: process all datasets jointly</option>
+        <option value="yes">Yes: process each dataset in an independent job</option>
+      </param>
+      <when value="no">
+        <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
+      </when>
+    </conditional>
+    <param argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/>
+    <param argument="-out_type" display="radio" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="idXML">idxml</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param name="protein_fdr" argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level based on the posteriors" help=""/>
-    <param name="greedy_group_resolution" argument="-greedy_group_resolution" display="radio" type="select" optional="false" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
+    <param argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level based on the posteriors" help=""/>
+    <param argument="-greedy_group_resolution" type="select" optional="true" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
       <option value="none" selected="true">none</option>
       <option value="remove_associations_only">remove_associations_only</option>
       <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="greedy_group_resolution"/>
     </param>
-    <param name="max_psms_extreme_probability" argument="-max_psms_extreme_probability" type="float" optional="true" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/>
+    <param argument="-max_psms_extreme_probability" type="float" optional="true" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/>
     <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false">
       <param name="psm_probability_cutoff" argument="-algorithm:psm_probability_cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.001" label="Remove PSMs with probabilities less than this cutoff" help=""/>
       <param name="top_PSMs" argument="-algorithm:top_PSMs" type="integer" optional="true" min="0" value="1" label="Consider only top X PSMs per spectrum" help="0 considers all"/>
@@ -81,13 +99,13 @@
         <param name="extended_model" argument="-algorithm:model_parameters:extended_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses information from different peptidoforms also across runs (automatically activated if an experimental design is given!)" help=""/>
       </section>
       <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false">
-        <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" display="radio" type="select" optional="false" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
+        <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" optional="true" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
           <option value="priority" selected="true">priority</option>
           <option value="fifo">fifo</option>
           <option value="subtree">subtree</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="scheduling_type"/>
         </param>
-        <param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" optional="true" min="1e-09" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/>
+        <param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/>
         <param name="dampening_lambda" argument="-algorithm:loopy_belief_propagation:dampening_lambda" type="float" optional="true" min="0.0" max="0.49999" value="0.001" label="Initial value for how strongly should messages be updated in each step" help="0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence"/>
         <param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" optional="true" value="2147483647" label="(Usually auto-determined by estimated but you can set a hard limit here)" help="If not all messages converge, how many iterations should be done at max per connected component?"/>
         <param name="p_norm_inference" argument="-algorithm:loopy_belief_propagation:p_norm_inference" type="float" optional="true" value="1.0" label="P-norm used for marginalization of multidimensional factors" help="1 == sum-product inference (all configurations vote equally) (default),&lt;= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/>
@@ -99,11 +117,20 @@
       </section>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="conservative_fdr" argument="-conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs" help=""/>
-      <param name="min_psms_extreme_probability" argument="-min_psms_extreme_probability" type="float" optional="true" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <param argument="-conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs" help=""/>
+      <param argument="-picked_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use picked protein FDRs" help=""/>
+      <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection">
+        <expand macro="list_string_san" name="picked_decoy_string"/>
+      </param>
+      <param argument="-picked_decoy_prefix" type="select" optional="true" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
+        <option value="prefix" selected="true">prefix</option>
+        <option value="suffix">suffix</option>
+        <expand macro="list_string_san" name="picked_decoy_prefix"/>
+      </param>
+      <param argument="-min_psms_extreme_probability" type="float" optional="true" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -111,9 +138,8 @@
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out">
+    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
       <change_format>
-        <when input="out_type" value="consensusXML" format="consensusxml"/>
         <when input="out_type" value="idXML" format="idxml"/>
       </change_format>
     </data>
@@ -121,13 +147,285 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_Epifany"/>
-    <expand macro="manutest_Epifany"/>
+  <tests><!-- UTILS_Epifany_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="conservative_fdr" value="true"/>
+        <param name="picked_fdr" value="true"/>
+        <param name="picked_decoy_string" value=""/>
+        <param name="picked_decoy_prefix" value="prefix"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FidoAdapter_1_input.idXML"/>
+      </conditional>
+      <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_Epifany_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="conservative_fdr" value="true"/>
+        <param name="picked_fdr" value="true"/>
+        <param name="picked_decoy_string" value=""/>
+        <param name="picked_decoy_prefix" value="prefix"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="Epifany_2_input.consensusXML"/>
+      </conditional>
+      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_Epifany_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="conservative_fdr" value="true"/>
+        <param name="picked_fdr" value="true"/>
+        <param name="picked_decoy_string" value=""/>
+        <param name="picked_decoy_prefix" value="prefix"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="Epifany_2_input.consensusXML"/>
+      </conditional>
+      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="false"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_Epifany_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="conservative_fdr" value="true"/>
+        <param name="picked_fdr" value="true"/>
+        <param name="picked_decoy_string" value=""/>
+        <param name="picked_decoy_prefix" value="prefix"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/>
+      </conditional>
+      <output name="out" file="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_Epifany_5 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="conservative_fdr" value="true"/>
+        <param name="picked_fdr" value="false"/>
+        <param name="picked_decoy_string" value=""/>
+        <param name="picked_decoy_prefix" value="prefix"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/>
+      </conditional>
+      <output name="out" file="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="protein_fdr" value="true"/>
+      <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Runs a Bayesian protein inference.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_Epifany.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Epifany.html]]></help>
   <expand macro="references"/>
 </tool>