--- a/SpecLibCreator.xml	Thu Dec 01 19:07:29 2022 +0000
+++ b/SpecLibCreator.xml	Fri Jun 14 21:37:55 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: [Identification Processing]-->
 <tool id="SpecLibCreator" name="SpecLibCreator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Creates an MSP formatted spectral library.</description>
+  <description>Creates an MSP formatted spectral library</description>
   <macros>
     <token name="@EXECUTABLE@">SpecLibCreator</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir info &&
-ln -s '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' &&
+cp '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' &&
 mkdir spec &&
-ln -s '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' &&
+cp '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' &&
 mkdir out &&
 
 ## 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="-info" type="data" format="csv" optional="false" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
-    <param argument="-itemseperator" type="text" optional="true" value="," label=" Separator between items. e.g. ," help="">
+    <param argument="-info" type="data" format="csv" label="Holds id, peptide, retention time etc" help=" select csv data sets(s)"/>
+    <param argument="-itemseperator" type="text" value="," label=" Separator between items. e.g. ," help="">
       <expand macro="list_string_san" name="itemseperator"/>
     </param>
     <param argument="-itemenclosed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="'true' or 'false' if true every item is enclosed" help="e.g. '$peptide$,$run$"/>
-    <param argument="-spec" type="data" format="mzdata,mzxml" optional="false" label="spectra" help=" select mzdata,mzxml data sets(s)"/>
+    <param argument="-spec" type="data" format="mzdata,mzxml" label="spectra" help=" select mzdata,mzxml 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 could not find test data -->
-</tests>
+  <tests>
+    <!--TODO could not find test data -->
+  </tests>
   <help><![CDATA[Creates an MSP formatted spectral library.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpecLibCreator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpecLibCreator.html]]></help>
   <expand macro="references"/>
 </tool>