--- a/TriqlerConverter.xml	Thu Dec 01 19:22:27 2022 +0000
+++ b/TriqlerConverter.xml	Fri Jun 14 21:41:43 2024 +0000
@@ -1,6 +1,5 @@
-<?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]-->
+<!--Proposed Tool Section: [File Converter]-->
 <tool id="TriqlerConverter" name="TriqlerConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Converter to input for Triqler</description>
   <macros>
@@ -15,20 +14,22 @@
 
 ## 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($in.ext)' &&
 mkdir in_design &&
-ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
+cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
 mkdir out &&
+## advanced options
   #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
     mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
     #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
     mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && 
-    ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
+    ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
     #else
-    ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
+    cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
     #end if
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -41,6 +42,7 @@
 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
 -out
 'out/output.${gxy2omsext("csv")}'
+## advanced options
   #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
     -reannotate_filenames
     #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
@@ -50,6 +52,7 @@
     #end if
   #end if
 
+
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("csv")}' '$out'
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
@@ -60,9 +63,9 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
-    <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
-    <param argument="-Triqler_condition" type="text" optional="true" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help="">
+    <param argument="-in" type="data" format="consensusxml" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_design" type="data" format="tabular" label="Experimental Design file" help=" select tabular data sets(s)"/>
+    <param argument="-Triqler_condition" type="text" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help="">
       <expand macro="list_string_san" name="Triqler_condition"/>
     </param>
     <expand macro="adv_opts_macro">
@@ -75,11 +78,11 @@
           <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
         </when>
         <when value="yes">
-          <param argument="-reannotate_filenames" type="data" format="mzml" multiple="false" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+          <param argument="-reannotate_filenames" type="data" format="mzml" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
         </when>
       </conditional>
       <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>
@@ -97,6 +100,6 @@
   <help><![CDATA[Converter to input for Triqler
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TriqlerConverter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TriqlerConverter.html]]></help>
   <expand macro="references"/>
 </tool>