--- a/OpenSwathRewriteToFeatureXML.xml	Thu Dec 01 19:23:47 2022 +0000
+++ b/OpenSwathRewriteToFeatureXML.xml	Fri Jun 14 21:34:21 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: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
+  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
     <import>macros.xml</import>
@@ -16,10 +15,10 @@
 ## Preprocessing
 #if $csv:
   mkdir csv &&
-  ln -s '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
+  cp '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
 #end if
 mkdir featureXML &&
-ln -s '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
+cp '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -48,11 +47,11 @@
   </configfiles>
   <inputs>
     <param argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
-    <param argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/>
-    <param argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
+    <param argument="-featureXML" type="data" format="featurexml" label="input featureXML file" help=" select featurexml data sets(s)"/>
+    <param argument="-FDR_cutoff" type="float" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
     <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>
@@ -66,15 +65,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-    <param name="adv_opts|test" value="true"/>
-    <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- same input as used in the MSGF+Adapter -->
+      <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
+      <param name="adv_opts|test" value="true"/>
+      <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
+    </test>
+  </tests>
   <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRewriteToFeatureXML.html]]></help>
   <expand macro="references"/>
 </tool>