--- a/IDPosteriorErrorProbability.xml	Thu Dec 01 18:59:09 2022 +0000
+++ b/IDPosteriorErrorProbability.xml	Fri Jun 14 21:40:19 2024 +0000
@@ -1,8 +1,7 @@
-<?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: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
+  <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model</description>
   <macros>
     <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_plot &&
@@ -52,21 +51,21 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
     <param argument="-split_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The search engine scores are split by charge if this flag is set" help="Thus, for each charge state a new model will be computed"/>
     <param argument="-top_hits_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set only the top hits of every PeptideIdentification will be used" help=""/>
     <param argument="-ignore_bad_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set errors will be written but ignored" help="Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/>
     <param argument="-prob_correct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help=""/>
     <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" optional="true" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
-      <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" optional="true" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
+      <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
+      <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
         <option value="Gumbel" selected="true">Gumbel</option>
         <option value="Gauss">Gauss</option>
         <expand macro="list_string_san" name="incorrectly_assigned"/>
       </param>
-      <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" optional="true" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
-      <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" optional="true" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
-      <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" optional="true" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
+      <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
+      <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
+      <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
         <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option>
         <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option>
         <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option>
@@ -75,9 +74,9 @@
       </param>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-fdr_for_targets_smaller" type="float" optional="true" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
+      <param argument="-fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
       <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="">
+      <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>
@@ -95,7 +94,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDPosteriorErrorProbability_1 -->
+  <tests>
+    <!-- TOPP_IDPosteriorErrorProbability_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="fdr_for_targets_smaller" value="0.05"/>
@@ -103,7 +103,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -121,6 +121,9 @@
           <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_IDPosteriorErrorProbability_2 -->
     <test expect_num_outputs="2">
@@ -130,7 +133,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -148,6 +151,9 @@
           <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_IDPosteriorErrorProbability_3 -->
     <test expect_num_outputs="2">
@@ -157,7 +163,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -175,6 +181,9 @@
           <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_IDPosteriorErrorProbability_4 -->
     <test expect_num_outputs="2">
@@ -184,7 +193,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="true"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -202,6 +211,9 @@
           <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_IDPosteriorErrorProbability_5 -->
     <test expect_num_outputs="2">
@@ -211,7 +223,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="true"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -229,6 +241,9 @@
           <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_IDPosteriorErrorProbability_6 -->
     <test expect_num_outputs="2">
@@ -238,7 +253,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="true"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -256,6 +271,9 @@
           <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_IDPosteriorErrorProbability_7 -->
     <test expect_num_outputs="2">
@@ -265,7 +283,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_bad_data_output.tmp" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="true"/>
@@ -283,6 +301,9 @@
           <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_IDPosteriorErrorProbability_8 -->
     <test expect_num_outputs="2">
@@ -292,7 +313,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="split_charge" value="false"/>
       <param name="top_hits_only" value="false"/>
       <param name="ignore_bad_data" value="false"/>
@@ -310,11 +331,14 @@
           <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[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDPosteriorErrorProbability.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDPosteriorErrorProbability.html]]></help>
   <expand macro="references"/>
 </tool>