--- a/OpenSwathFileSplitter.xml	Fri Nov 06 20:05:37 2020 +0000
+++ b/OpenSwathFileSplitter.xml	Thu Dec 01 19:02:09 2022 +0000
@@ -1,13 +1,11 @@
 <?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]-->
-<tool id="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<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>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathFileSplitter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -53,11 +51,11 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" 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" optional="false" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <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="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -67,7 +65,7 @@
   </inputs>
   <outputs>
     <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
-      <discover_datasets directory="outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+      <discover_datasets directory="outputDirectory" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
     <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
       <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
@@ -76,13 +74,28 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_OpenSwathFileSplitter"/>
-    <expand macro="manutest_OpenSwathFileSplitter"/>
-  </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/2.6.0/html/UTILS_OpenSwathFileSplitter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathFileSplitter.html]]></help>
   <expand macro="references"/>
 </tool>