--- a/QCMerger.xml	Thu Dec 01 19:01:48 2022 +0000
+++ b/QCMerger.xml	Fri Jun 14 21:35:44 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="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Merges two qcml files together.</description>
+  <description>Merges two qcml files together</description>
   <macros>
     <token name="@EXECUTABLE@">QCMerger</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 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
 mkdir out &&
 
@@ -54,10 +53,10 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="qcml" multiple="true" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
+        <param argument="-in" type="data" format="qcml" multiple="true" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="qcml" multiple="false" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
+        <param argument="-in" type="data" format="qcml" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help="">
@@ -65,7 +64,7 @@
     </param>
     <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>
@@ -79,15 +78,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
-    <output name="out" ftype="qcml" value="QCMerger.qcML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
+      <output name="out" ftype="qcml" value="QCMerger.qcML"/>
+    </test>
+  </tests>
   <help><![CDATA[Merges two qcml files together.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCMerger.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCMerger.html]]></help>
   <expand macro="references"/>
 </tool>