--- a/QualityControl.xml	Thu Dec 01 19:18:12 2022 +0000
+++ b/QualityControl.xml	Fri Jun 14 21:46:38 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: [Quality Control]-->
 <tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.</description>
+  <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get</description>
   <macros>
     <token name="@EXECUTABLE@">QualityControl</token>
     <import>macros.xml</import>
@@ -15,23 +14,23 @@
 
 ## Preprocessing
 mkdir in_cm &&
-ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
+cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
 #if $in_raw_cond.in_raw:
   mkdir in_raw_cond.in_raw &&
   #if $in_raw_cond.in_raw_select == "no"
   mkdir ${' '.join(["'in_raw_cond.in_raw/%s'" % (i) for i, f in enumerate($in_raw_cond.in_raw) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
+  ${' '.join(["cp '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
   #else
-  ln -s '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' &&
+  cp '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' &&
   #end if
 #end if
 #if $in_postFDR_cond.in_postFDR:
   mkdir in_postFDR_cond.in_postFDR &&
   #if $in_postFDR_cond.in_postFDR_select == "no"
   mkdir ${' '.join(["'in_postFDR_cond.in_postFDR/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
+  ${' '.join(["cp '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
   #else
-  ln -s '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' &&
+  cp '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' &&
   #end if
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -46,15 +45,19 @@
 #end if
 #if $in_contaminants:
   mkdir in_contaminants &&
-  ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
+  cp '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
+#end if
+#if $in_fasta:
+  mkdir in_fasta &&
+  cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
 #end if
 #if $in_trafo_cond.in_trafo:
   mkdir in_trafo_cond.in_trafo &&
   #if $in_trafo_cond.in_trafo_select == "no"
   mkdir ${' '.join(["'in_trafo_cond.in_trafo/%s'" % (i) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} && 
-  ${' '.join(["ln -s '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
+  ${' '.join(["cp '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
   #else
-  ln -s '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' &&
+  cp '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' &&
   #end if
 #end if
 
@@ -98,6 +101,10 @@
   -in_contaminants
   'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
 #end if
+#if $in_fasta:
+  -in_fasta
+  'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)'
+#end if
 #if $in_trafo_cond.in_trafo:
   -in_trafo
   #if $in_trafo_cond.in_trafo_select == "no"
@@ -128,7 +135,7 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_cm" type="data" format="consensusxml" optional="false" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_cm" type="data" format="consensusxml" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
     <conditional name="in_raw_cond">
       <param name="in_raw_select" type="select" label="Run tool in batch mode for -in_raw">
         <option value="no">No: process all datasets jointly</option>
@@ -138,7 +145,7 @@
         <param argument="-in_raw" type="data" format="mzml" multiple="true" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_raw" type="data" format="mzml" multiple="false" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
+        <param argument="-in_raw" type="data" format="mzml" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
     <conditional name="in_postFDR_cond">
@@ -150,10 +157,11 @@
         <param argument="-in_postFDR" type="data" format="featurexml" multiple="true" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_postFDR" type="data" format="featurexml" multiple="false" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
+        <param argument="-in_postFDR" type="data" format="featurexml" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/>
+    <param argument="-in_fasta" type="data" format="fasta" optional="true" label="FASTA file used during MS/MS identification (including decoys)" help="If the protein description contains 'GN=...' then gene names will be extracted select fasta data sets(s)"/>
     <conditional name="in_trafo_cond">
       <param name="in_trafo_select" type="select" label="Run tool in batch mode for -in_trafo">
         <option value="no">No: process all datasets jointly</option>
@@ -163,27 +171,30 @@
         <param argument="-in_trafo" type="data" format="trafoxml" multiple="true" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in_trafo" type="data" format="trafoxml" multiple="false" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
+        <param argument="-in_trafo" type="data" format="trafoxml" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-out_evd" type="text" optional="true" value="" label="If a Path is given, a MQEvidence txt-file will be created in this directory" help="If the directory does not exist, it will be created as well">
       <expand macro="list_string_san" name="out_evd"/>
     </param>
+    <param argument="-out_msms" type="text" optional="true" value="" label="If a Path is given, a MQMsms txt-file will be created in this directory" help="If the directory does not exist, it will be created as well">
+      <expand macro="list_string_san" name="out_msms"/>
+    </param>
     <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
-      <param name="unit" argument="-FragmentMassError:unit" type="select" optional="true" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
+      <param name="unit" argument="-FragmentMassError:unit" type="select" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
         <option value="auto" selected="true">auto</option>
         <option value="ppm">ppm</option>
         <option value="da">da</option>
         <expand macro="list_string_san" name="unit"/>
       </param>
-      <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" optional="true" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
+      <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
     </section>
     <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
       <param name="assume_all_target" argument="-MS2_id_rate:assume_all_target" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits)" help=""/>
     </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>
@@ -212,7 +223,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_QualityControl_1 -->
+  <tests>
+    <!-- TOPP_QualityControl_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -225,13 +237,15 @@
       <conditional name="in_postFDR_cond">
         <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
       </conditional>
-      <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
-      <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="QualityControl_1_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
+      <output name="out_cm" value="QualityControl_1_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="in_contaminants" value="QualityControl_1.fasta"/>
+      <param name="in_fasta" value="PeptideIndexer_1.fasta"/>
       <conditional name="in_trafo_cond">
         <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
       </conditional>
       <param name="out_evd" value=""/>
+      <param name="out_msms" value=""/>
       <section name="FragmentMassError">
         <param name="unit" value="auto"/>
         <param name="tolerance" value="20.0"/>
@@ -245,11 +259,14 @@
           <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[Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_QualityControl.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QualityControl.html]]></help>
   <expand macro="references"/>
 </tool>