--- a/QCImporter.xml	Thu Dec 01 19:23:03 2022 +0000
+++ b/QCImporter.xml	Fri Jun 14 21:38:55 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="QCImporter" name="QCImporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Imports tables with quality control parameters into qcml files.</description>
+  <description>Imports tables with quality control parameters into qcml files</description>
   <macros>
     <token name="@EXECUTABLE@">QCImporter</token>
     <import>macros.xml</import>
@@ -16,12 +15,12 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 mkdir table &&
-ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
+cp '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
 mkdir mapping &&
-ln -s '$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 &&
 
 ## Main program call
@@ -52,11 +51,11 @@
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
-    <param argument="-table" type="data" format="csv" optional="false" label="The table containing the additional qp values in the columns" help="First row is considered containing the header. The target run or set names/ids are indicated by column &quot;raw data file&quot;, so each row after the header will contain the values of qps for that run. (csv without &quot;!) select csv data sets(s)"/>
-    <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the table header to the according qp cvs, also in csv format" help="The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without &quot;!) select csv data sets(s)"/>
+    <param argument="-table" type="data" format="csv" label="The table containing the additional qp values in the columns" help="First row is considered containing the header. The target run or set names/ids are indicated by column &quot;raw data file&quot;, so each row after the header will contain the values of qps for that run. (csv without &quot;!) select csv data sets(s)"/>
+    <param argument="-mapping" type="data" format="csv" label="The mapping of the table header to the according qp cvs, also in csv format" help="The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without &quot;!) 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>
@@ -70,11 +69,12 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO-->
-</tests>
+  <tests>
+    <!--TODO-->
+  </tests>
   <help><![CDATA[Imports tables with quality control parameters into qcml files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCImporter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCImporter.html]]></help>
   <expand macro="references"/>
 </tool>