--- a/MRMMapper.xml	Fri Nov 06 20:34:11 2020 +0000
+++ b/MRMMapper.xml	Thu Dec 01 19:06:17 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="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
   <macros>
     <token name="@EXECUTABLE@">MRMMapper</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -45,8 +43,8 @@
     <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 containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
-    <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" optional="true" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
       <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" optional="true" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
@@ -54,9 +52,9 @@
       <param name="error_on_unmapped" argument="-algorithm:error_on_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat remaining, unmapped chromatograms as an erro" help=""/>
     </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">
@@ -69,13 +67,54 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MRMMapper"/>
-    <expand macro="manutest_MRMMapper"/>
+  <tests><!-- TOPP_MRMMapper_test_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="MRMMapping_input.chrom.mzML"/>
+      <param name="tr" value="MRMMapping_input.TraML"/>
+      <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="precursor_tolerance" value="0.3"/>
+        <param name="product_tolerance" value="0.3"/>
+        <param name="map_multiple_assays" value="false"/>
+        <param name="error_on_unmapped" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_MRMMapper_test_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="MRMMapping_input.chrom.mzML"/>
+      <param name="tr" value="MRMMapping_input_2.TraML"/>
+      <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <section name="algorithm">
+        <param name="precursor_tolerance" value="0.01"/>
+        <param name="product_tolerance" value="0.01"/>
+        <param name="map_multiple_assays" value="false"/>
+        <param name="error_on_unmapped" value="false"/>
+      </section>
+      <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[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MRMMapper.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MRMMapper.html]]></help>
   <expand macro="references"/>
 </tool>