--- a/ProteinResolver.xml	Thu Dec 01 18:57:06 2022 +0000
+++ b/ProteinResolver.xml	Fri Jun 14 21:31:23 2024 +0000
@@ -1,4 +1,3 @@
-<?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: [Quantitation]-->
 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
@@ -15,19 +14,19 @@
 
 ## Preprocessing
 mkdir fasta &&
-ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
+cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
 #if $in_cond.in:
   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
 #end if
 #if $design:
   mkdir design &&
-  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
+  cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir protein_groups &&
@@ -103,7 +102,7 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/>
+    <param argument="-fasta" type="data" format="fasta" label="Input database file" help=" select fasta data sets(s)"/>
     <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>
@@ -113,7 +112,7 @@
         <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,idxml" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given">
@@ -121,21 +120,21 @@
     </param>
     <param argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/>
     <section name="resolver" title="Additional options for algorithm" help="" expanded="false">
-      <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
-      <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/>
-      <param name="enzyme" argument="-resolver:enzyme" type="select" optional="true" label="Digestion enzyme" help="">
+      <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
+      <param name="min_length" argument="-resolver:min_length" type="integer" min="1" value="6" label="Minimum length of peptide" help=""/>
+      <param name="enzyme" argument="-resolver:enzyme" type="select" label="Digestion enzyme" help="">
         <option value="Trypsin" selected="true">Trypsin</option>
         <expand macro="list_string_san" name="enzyme"/>
       </param>
     </section>
     <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false">
-      <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
+      <param name="experiment" argument="-designer:experiment" type="text" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
         <expand macro="list_string_san" name="experiment"/>
       </param>
-      <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help="">
+      <param name="file" argument="-designer:file" type="text" value="File" label="Identifier for the file name" help="">
         <expand macro="list_string_san" name="file"/>
       </param>
-      <param name="separator" argument="-designer:separator" type="select" optional="true" label="Separator, which should be used to split a row into columns" help="">
+      <param name="separator" argument="-designer:separator" type="select" label="Separator, which should be used to split a row into columns" help="">
         <option value="tab" selected="true">tab</option>
         <option value="semi-colon">semi-colon</option>
         <option value="comma">comma</option>
@@ -145,7 +144,7 @@
     </section>
     <expand macro="adv_opts_macro">
       <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>
@@ -177,7 +176,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ProteinResolver_1 -->
+  <tests>
+    <!-- TOPP_ProteinResolver_1 -->
     <test expect_num_outputs="4">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -188,9 +188,9 @@
         <param name="in" value="ProteinResolver_1_input.consensusXML"/>
       </conditional>
       <param name="in_path" value=""/>
-      <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="protein_groups" value="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="peptide_table" value="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="protein_table" value="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <section name="resolver">
         <param name="missed_cleavages" value="2"/>
         <param name="min_length" value="6"/>
@@ -207,11 +207,14 @@
           <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
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinResolver.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinResolver.html]]></help>
   <expand macro="references"/>
 </tool>