--- a/MRMPairFinder.xml	Thu Dec 01 19:00:25 2022 +0000
+++ b/MRMPairFinder.xml	Fri Jun 14 21:43:58 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: [Targeted Experiments and OpenSWATH]-->
 <tool id="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
+  <description>Util which can be used to evaluate labeled pair ratios on MRM features</description>
   <macros>
     <token name="@EXECUTABLE@">MRMPairFinder</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## 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($in.ext)' &&
 mkdir pair_in &&
-ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
+cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
 mkdir out &&
 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir feature_out &&
@@ -56,14 +55,14 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml" optional="false" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
-    <param argument="-pair_in" type="data" format="csv" optional="false" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
+    <param argument="-in" type="data" format="featurexml" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
+    <param argument="-pair_in" type="data" format="csv" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
     <expand macro="adv_opts_macro">
-      <param argument="-mass_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
-      <param argument="-RT_tolerance" type="float" optional="true" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
-      <param argument="-RT_pair_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/>
+      <param argument="-mass_tolerance" type="float" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
+      <param argument="-RT_tolerance" type="float" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
+      <param argument="-RT_pair_tolerance" type="float" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" 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>
@@ -81,11 +80,12 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TODO no idea about a useful input for pair_in -->
-</tests>
+  <tests>
+    <!-- TODO no idea about a useful input for pair_in -->
+  </tests>
   <help><![CDATA[Util which can be used to evaluate labeled pair ratios on MRM features.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMPairFinder.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMPairFinder.html]]></help>
   <expand macro="references"/>
 </tool>