--- a/MzMLSplitter.xml	Fri Nov 06 20:01:29 2020 +0000
+++ b/MzMLSplitter.xml	Thu Dec 01 19:14:47 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: [Utilities]-->
-<tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Splits an mzML file into multiple parts</description>
   <macros>
     <token name="@EXECUTABLE@">MzMLSplitter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -40,21 +38,21 @@
     <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" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param name="parts" argument="-parts" type="integer" optional="true" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
-    <param name="size" argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
-    <param name="unit" argument="-unit" display="radio" type="select" optional="false" label="Unit for 'size' (base 1024)" help="">
+    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
+    <param argument="-parts" type="integer" optional="true" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
+    <param argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
+    <param argument="-unit" type="select" optional="true" label="Unit for 'size' (base 1024)" help="">
       <option value="KB">KB</option>
       <option value="MB" selected="true">MB</option>
       <option value="GB">GB</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="unit"/>
     </param>
-    <param name="no_chrom" argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/>
-    <param name="no_spec" argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/>
+    <param argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/>
+    <param argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/>
     <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">
@@ -63,19 +61,60 @@
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+      <discover_datasets directory="out" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MzMLSplitter"/>
-    <expand macro="manutest_MzMLSplitter"/>
-  </tests>
+  <tests><!-- UTILS_MzMLSplitter_1 -->
+    <!-- UTILS_MzMLSplitter_2 -->
+  <test expect_num_outputs="2">
+  <section name="adv_opts">
+    <param name="test" value="true"/>
+  </section>
+  <param name="in" value="FileFilter_1_input.mzML"/>
+  <param name="parts" value="2"/>
+  <param name="size" value="0"/>
+  <param name="unit" value="MB"/>
+  <param name="no_chrom" value="false"/>
+  <param name="no_spec" value="false"/>
+  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+  <output name="ctd_out" ftype="xml">
+    <assert_contents>
+      <is_valid_xml/>
+    </assert_contents>
+  </output>
+  <output_collection name="out" type="list" count="2">
+    <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
+    <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
+  </output_collection>
+</test>
+<test expect_num_outputs="2">
+  <section name="adv_opts">
+    <param name="test" value="true"/>
+  </section>
+  <param name="in" value="FileFilter_1_input.mzML"/>
+  <param name="parts" value="1"/>
+  <param name="size" value="40"/>
+  <param name="unit" value="KB"/>
+  <param name="no_chrom" value="false"/>
+  <param name="no_spec" value="false"/>
+  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+  <output name="ctd_out" ftype="xml">
+    <assert_contents>
+      <is_valid_xml/>
+    </assert_contents>
+  </output>
+  <output_collection name="out" type="list" count="2">
+    <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
+    <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
+  </output_collection>
+</test>
+</tests>
   <help><![CDATA[Splits an mzML file into multiple parts
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MzMLSplitter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MzMLSplitter.html]]></help>
   <expand macro="references"/>
 </tool>