--- a/ERPairFinder.xml	Thu Dec 01 19:06:06 2022 +0000
+++ b/ERPairFinder.xml	Fri Jun 14 21:34:13 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: [Quantitation]-->
 <tool id="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
+  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans</description>
   <macros>
     <token name="@EXECUTABLE@">ERPairFinder</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 &&
@@ -56,17 +55,17 @@
     <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 mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
-    <param argument="-pair_in" type="data" format="txt" optional="false" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" 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="-in" type="data" format="mzml" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
+    <param argument="-pair_in" type="data" format="txt" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
+    <param argument="-precursor_mass_tolerance" type="float" min="0.0" value="0.3" 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=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-RT_tolerance" type="float" optional="true" min="1.0" 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="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
-      <param argument="-intensity_threshold" type="float" optional="true" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/>
-      <param argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
-      <param argument="-expansion_range" type="float" optional="true" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/>
+      <param argument="-RT_tolerance" type="float" min="1.0" 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="-max_charge" type="integer" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
+      <param argument="-intensity_threshold" type="float" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/>
+      <param argument="-max_isotope" type="integer" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
+      <param argument="-expansion_range" type="float" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" 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>
@@ -84,11 +83,12 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TODO -->
-</tests>
+  <tests>
+    <!-- TODO -->
+  </tests>
   <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ERPairFinder.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ERPairFinder.html]]></help>
   <expand macro="references"/>
 </tool>