--- a/ProteinInference.xml	Thu Dec 01 19:00:46 2022 +0000
+++ b/ProteinInference.xml	Fri Jun 14 21:29:31 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: [Identification]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="ProteinInference" name="ProteinInference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Protein inference based on an aggregation of the scores of the identified peptides.</description>
+  <description>Protein inference based on an aggregation of the scores of the identified peptides</description>
   <macros>
     <token name="@EXECUTABLE@">ProteinInference</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 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])}
+${' '.join(["cp '%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($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 
@@ -54,18 +53,19 @@
         <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 file(s)" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" label="input file(s)" 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 file(s)" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="output file type" help="">
+    <param argument="-out_type" type="select" label="output file type" help="">
       <option value="consensusXML">consensusxml</option>
       <option value="idXML">idxml</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="-merge_runs" type="select" optional="true" label="If your idXML contains multiple runs, merge them beforehand" help="Otherwise performs inference separately per run">
+    <param argument="-merge_runs" type="select" label="If your idXML contains multiple runs, merge them beforehand" help="Otherwise performs inference separately per run">
       <option value="no">no</option>
       <option value="all" selected="true">all</option>
       <expand macro="list_string_san" name="merge_runs"/>
@@ -76,8 +76,8 @@
       <param name="allow_disagreeing_settings" argument="-Merging:allow_disagreeing_settings" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force merging of disagreeing runs" help="Use at your own risk"/>
     </section>
     <section name="Algorithm" title="" help="" expanded="false">
-      <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="true" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
-      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" type="select" optional="true" label="How to aggregate scores of peptides matching to the same protein?" help="">
+      <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
+      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" type="select" label="How to aggregate scores of peptides matching to the same protein?" help="">
         <option value="best" selected="true">best</option>
         <option value="product">product</option>
         <option value="sum">sum</option>
@@ -97,13 +97,13 @@
       <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">
+      <param argument="-picked_decoy_prefix" type="select" 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="-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>
@@ -121,7 +121,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ProteinInference_1 -->
+  <tests>
+    <!-- TOPP_ProteinInference_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="conservative_fdr" value="true"/>
@@ -134,7 +135,7 @@
       <conditional name="in_cond">
         <param name="in" value="ProteinInference_1_input.idXML"/>
       </conditional>
-      <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="ProteinInference_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="merge_runs" value="all"/>
       <param name="protein_fdr" value="false"/>
@@ -158,6 +159,9 @@
           <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_ProteinInference_2 -->
     <test expect_num_outputs="2">
@@ -172,7 +176,7 @@
       <conditional name="in_cond">
         <param name="in" value="Epifany_2_input.consensusXML"/>
       </conditional>
-      <output name="out" file="ProteinInference_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="ProteinInference_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="merge_runs" value="all"/>
       <param name="protein_fdr" value="false"/>
@@ -196,6 +200,9 @@
           <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_ProteinInference_3 -->
     <test expect_num_outputs="2">
@@ -210,7 +217,7 @@
       <conditional name="in_cond">
         <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
       </conditional>
-      <output name="out" file="ProteinInference_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="ProteinInference_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="out_type" value="consensusXML"/>
       <param name="merge_runs" value="all"/>
       <param name="protein_fdr" value="true"/>
@@ -234,11 +241,14 @@
           <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[Protein inference based on an aggregation of the scores of the identified peptides.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinInference.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinInference.html]]></help>
   <expand macro="references"/>
 </tool>