--- a/DeMeanderize.xml	Thu Dec 01 19:01:59 2022 +0000
+++ b/DeMeanderize.xml	Fri Jun 14 21:38:10 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: [Misc / Helpers]-->
 <tool id="DeMeanderize" name="DeMeanderize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Orders the spectra of MALDI spotting plates correctly.</description>
+  <description>Orders the spectra of MALDI spotting plates correctly</description>
   <macros>
     <token name="@EXECUTABLE@">DeMeanderize</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
@@ -39,12 +38,12 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/>
-    <param argument="-num_spots_per_row" type="integer" optional="true" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/>
+    <param argument="-in" type="data" format="mzml" label="Input experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/>
+    <param argument="-num_spots_per_row" type="integer" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-RT_distance" type="float" optional="true" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/>
+      <param argument="-RT_distance" type="float" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/>
       <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>
@@ -58,15 +57,10 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
-	<output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
-  </test>
-</tests>
+  <tests/>
   <help><![CDATA[Orders the spectra of MALDI spotting plates correctly.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DeMeanderize.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DeMeanderize.html]]></help>
   <expand macro="references"/>
 </tool>