--- a/SpectraMerger.xml	Fri Nov 06 19:58:11 2020 +0000
+++ b/SpectraMerger.xml	Thu Dec 01 19:03:02 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: [Signal processing and preprocessing]-->
-<tool id="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraMerger</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,55 +39,55 @@
     <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 mzML file" help=" select mzml data sets(s)"/>
-    <param name="merging_method" argument="-merging_method" display="radio" type="select" optional="false" label="Method of merging which should be used" help="">
+    <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-merging_method" type="select" optional="true" label="Method of merging which should be used" help="">
       <option value="average_gaussian" selected="true">average_gaussian</option>
       <option value="average_tophat">average_tophat</option>
       <option value="precursor_method">precursor_method</option>
       <option value="block_method">block_method</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="merging_method"/>
     </param>
     <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false">
       <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" optional="true" min="0.0" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="Closer data points or peaks will be merged"/>
-      <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" display="radio" type="select" optional="false" label="Unit in which the distance between two data points or peaks is given" help="">
+      <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" optional="true" label="Unit in which the distance between two data points or peaks is given" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="mz_binning_width_unit"/>
       </param>
-      <param name="sort_blocks" argument="-algorithm:sort_blocks" display="radio" type="select" optional="false" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
+      <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" optional="true" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
         <option value="RT_ascending" selected="true">RT_ascending</option>
-        <option value=" RT_descending"> RT_descending</option>
-        <expand macro="list_string_san"/>
+        <option value="RT_descending">RT_descending</option>
+        <expand macro="list_string_san" name="sort_blocks"/>
       </param>
       <section name="average_gaussian" title="" help="" expanded="false">
-        <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" display="radio" type="select" optional="false" label="Spectrum type of the MS level to be averaged" help="">
+        <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" optional="true" label="Spectrum type of the MS level to be averaged" help="">
           <option value="profile">profile</option>
           <option value="centroid">centroid</option>
           <option value="automatic" selected="true">automatic</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="spectrum_type"/>
         </param>
         <param name="ms_level" argument="-algorithm:average_gaussian:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/>
         <param name="rt_FWHM" argument="-algorithm:average_gaussian:rt_FWHM" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help=""/>
         <param name="cutoff" argument="-algorithm:average_gaussian:cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Intensity cutoff for Gaussian" help="The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
       </section>
       <section name="average_tophat" title="" help="" expanded="false">
-        <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" display="radio" type="select" optional="false" label="Spectrum type of the MS level to be averaged" help="">
+        <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" optional="true" label="Spectrum type of the MS level to be averaged" help="">
           <option value="profile">profile</option>
           <option value="centroid">centroid</option>
           <option value="automatic" selected="true">automatic</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="spectrum_type"/>
         </param>
         <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/>
         <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="RT range to be averaged ove" help="i.e. +/-(RT range)/2 from each spectrum"/>
-        <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" display="radio" type="select" optional="false" label="Unit for RT range" help="">
+        <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" optional="true" label="Unit for RT range" help="">
           <option value="scans" selected="true">scans</option>
           <option value="seconds">seconds</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="rt_unit"/>
         </param>
       </section>
       <section name="block_method" title="" help="" expanded="false">
         <param name="ms_levels" argument="-algorithm:block_method:ms_levels" type="text" optional="true" value="1" label="Merge spectra of this level" help="All spectra with other MS levels remain untouched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
-          <expand macro="list_integer_valsan">
+          <expand macro="list_integer_valsan" name="ms_levels">
             <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if  1 <= int(_)])
 ]]></validator>
           </expand>
@@ -103,9 +101,9 @@
       </section>
     </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">
@@ -118,13 +116,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SpectraMerger"/>
-    <expand macro="manutest_SpectraMerger"/>
-  </tests>
+  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
+    <param name="adv_opts|test" value="true"/>
+    <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
+    <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
+  </test>
+</tests>
   <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpectraMerger.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraMerger.html]]></help>
   <expand macro="references"/>
 </tool>