--- a/MetaboliteSpectralMatcher.xml	Fri Nov 06 20:22:22 2020 +0000
+++ b/MetaboliteSpectralMatcher.xml	Thu Dec 01 19:02:30 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="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Perform a spectral library search.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -45,31 +43,31 @@
     <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 spectra" help=" select mzml data sets(s)"/>
-    <param name="database" argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/>
+    <param argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/>
       <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/>
-      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="mass_error_unit"/>
       </param>
-      <param name="report_mode" argument="-algorithm:report_mode" display="radio" type="select" optional="false" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
+      <param name="report_mode" argument="-algorithm:report_mode" type="select" optional="true" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
         <option value="top3" selected="true">top3</option>
         <option value="best">best</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="report_mode"/>
       </param>
-      <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode?" help="">
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode?" help="">
         <option value="positive" selected="true">positive</option>
         <option value="negative">negative</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="ionization_mode"/>
       </param>
     </section>
     <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">
@@ -82,13 +80,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MetaboliteSpectralMatcher"/>
-    <expand macro="manutest_MetaboliteSpectralMatcher"/>
-  </tests>
+  <tests><!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
+  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" ftype="mzml" value="spectra.mzML"/>
+    <param name="database" value="MetaboliteSpectralDB.mzML"/>
+    <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
+  </test>
+</tests>
   <help><![CDATA[Perform a spectral library search.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help>
   <expand macro="references"/>
 </tool>