--- a/MapStatistics.xml	Thu Dec 01 19:16:16 2022 +0000
+++ b/MapStatistics.xml	Fri Jun 14 21:33:50 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: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="MapStatistics" name="MapStatistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extract extended statistics on the features of a map for quality control.</description>
+  <description>Extract extended statistics on the features of a map for quality control</description>
   <macros>
     <token name="@EXECUTABLE@">MapStatistics</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## 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 out &&
 
 ## Main program call
@@ -39,14 +38,14 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
-    <param argument="-n" type="integer" optional="true" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
+    <param argument="-in" type="data" format="consensusxml,featurexml" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
+    <param argument="-n" type="integer" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
     <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
     <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
     <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/>
     <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>
@@ -60,20 +59,23 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with a featureXML input  -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
-    <output name="out" ftype="txt" value="MapStatistics.txt"/>
-  </test>
-  <test expect_num_outputs="1"><!-- test with a consensusxml input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
-    <output name="out" ftype="txt" value="MapStatistics2.txt"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- test with a featureXML input  -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
+      <output name="out" ftype="txt" value="MapStatistics.txt"/>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- test with a consensusxml input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
+      <output name="out" ftype="txt" value="MapStatistics2.txt"/>
+    </test>
+  </tests>
   <help><![CDATA[Extract extended statistics on the features of a map for quality control.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapStatistics.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapStatistics.html]]></help>
   <expand macro="references"/>
 </tool>