--- a/QCExporter.xml	Thu Dec 01 19:15:54 2022 +0000
+++ b/QCExporter.xml	Fri Jun 14 21:31:54 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: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Will extract several qp from several run/sets in a tabular format.</description>
+  <description>Will extract several qp from several run/sets in a tabular format</description>
   <macros>
     <token name="@EXECUTABLE@">QCExporter</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## 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($in.ext)' &&
 mkdir mapping &&
-ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
+cp '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
 mkdir out_csv &&
 
 ## Main program call
@@ -43,15 +42,15 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/>
     <param argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="names"/>
       <expand macro="list_string_san" name="names"/>
     </param>
-    <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv data sets(s)"/>
+    <param argument="-mapping" type="data" format="csv" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv data sets(s)"/>
     <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>
@@ -65,11 +64,12 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO-->
-</tests>
+  <tests>
+    <!--TODO-->
+  </tests>
   <help><![CDATA[Will extract several qp from several run/sets in a tabular format.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCExporter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCExporter.html]]></help>
   <expand macro="references"/>
 </tool>