--- a/OpenSwathFileSplitter.xml	Thu Dec 01 19:02:09 2022 +0000
+++ b/OpenSwathFileSplitter.xml	Fri Jun 14 21:45:22 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="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Splits SWATH files into n files, each containing one window.</description>
+  <description>Splits SWATH files into n files, each containing one window</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathFileSplitter</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($in.ext)' &&
 mkdir outputDirectory &&
 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_qc &&
@@ -51,10 +50,10 @@
     <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,mzxml" optional="false" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml,mzxml" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
     <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>
@@ -74,28 +73,29 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathFileSplitter_1 -->
-  <test expect_num_outputs="3">
-    <section name="adv_opts">
-      <param name="test" value="true"/>
-    </section>
-    <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
-    <output_collection name="outputDirectory" count="6">
-      <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
-      <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
-    </output_collection>
-    <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
-    <output name="ctd_out" ftype="xml">
-      <assert_contents>
-        <is_valid_xml/>
-      </assert_contents>
-    </output>
-  </test>
-</tests>
+  <tests>
+    <!-- TOPP_OpenSwathFileSplitter_1 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+      <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
+      <output_collection name="outputDirectory" count="6">
+        <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
+        <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
+      </output_collection>
+      <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
   <help><![CDATA[Splits SWATH files into n files, each containing one window.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathFileSplitter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathFileSplitter.html]]></help>
   <expand macro="references"/>
 </tool>