--- a/CVInspector.xml	Thu Dec 01 18:56:45 2022 +0000
+++ b/CVInspector.xml	Fri Jun 14 21:28:01 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: [[for Developers]]-->
 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>A tool for visualization and validation of PSI mapping and CV files.</description>
+  <description>A tool for visualization and validation of PSI mapping and CV files</description>
   <macros>
     <token name="@EXECUTABLE@">CVInspector</token>
     <import>macros.xml</import>
@@ -17,12 +16,12 @@
 mkdir cv_files_cond.cv_files &&
 #if $cv_files_cond.cv_files_select == "no"
 mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} && 
-${' '.join(["ln -s '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
+${' '.join(["cp '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
 #else
-ln -s '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
+cp '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
 #end if
 mkdir mapping_file &&
-ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
+cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir html &&
 #end if
@@ -67,24 +66,24 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-cv_files" type="data" format="obo" multiple="true" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
+        <param argument="-cv_files" type="data" format="obo" multiple="true" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-cv_files" type="data" format="obo" multiple="false" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
+        <param argument="-cv_files" type="data" format="obo" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-cv_names" type="text" optional="false" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-cv_names" type="text" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="cv_names"/>
       <expand macro="list_string_san" name="cv_names"/>
     </param>
-    <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
-    <param argument="-ignore_cv" type="text" optional="true" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-mapping_file" type="data" format="xml" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
+    <param argument="-ignore_cv" type="text" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="ignore_cv"/>
       <expand macro="list_string_san" name="ignore_cv"/>
     </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>
@@ -104,19 +103,20 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml -->
-  <test expect_num_outputs="1">
-    <param name="adv_opts|test" value="true"/>
-    <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
-    <param name="cv_names" value="XLMOD"/>
-    <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
-    <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
-    <output name="html" ftype="html" value="CVInspector.html"/>
-  </test>
-</tests>
+  <tests>
+    <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml -->
+    <test expect_num_outputs="1">
+      <param name="adv_opts|test" value="true"/>
+      <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
+      <param name="cv_names" value="XLMOD"/>
+      <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
+      <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
+      <output name="html" ftype="html" value="CVInspector.html"/>
+    </test>
+  </tests>
   <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_CVInspector.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CVInspector.html]]></help>
   <expand macro="references"/>
 </tool>