--- a/BaselineFilter.xml	Fri Nov 06 19:45:22 2020 +0000
+++ b/BaselineFilter.xml	Thu Dec 01 19:10:21 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="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Removes the baseline from profile spectra using a top-hat filter.</description>
   <macros>
     <token name="@EXECUTABLE@">BaselineFilter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -41,14 +39,14 @@
     <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 raw data file" help=" select mzml data sets(s)"/>
-    <param name="struc_elem_length" argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
-    <param name="struc_elem_unit" argument="-struc_elem_unit" display="radio" type="select" optional="false" label="Unit of 'struc_elem_length' paramete" help="">
+    <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
+    <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help="">
       <option value="Thomson" selected="true">Thomson</option>
       <option value="DataPoints">DataPoints</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="struc_elem_unit"/>
     </param>
-    <param name="method" argument="-method" type="select" optional="false" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
+    <param argument="-method" type="select" optional="true" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
       <option value="identity">identity</option>
       <option value="erosion">erosion</option>
       <option value="dilation">dilation</option>
@@ -59,12 +57,12 @@
       <option value="bothat">bothat</option>
       <option value="erosion_simple">erosion_simple</option>
       <option value="dilation_simple">dilation_simple</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="method"/>
     </param>
     <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">
@@ -77,13 +75,28 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_BaselineFilter"/>
-    <expand macro="manutest_BaselineFilter"/>
+  <tests><!-- TOPP_BaselineFilter_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="BaselineFilter_input.mzML"/>
+      <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <param name="struc_elem_length" value="1.5"/>
+      <param name="struc_elem_unit" value="Thomson"/>
+      <param name="method" value="tophat"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_BaselineFilter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_BaselineFilter.html]]></help>
   <expand macro="references"/>
 </tool>