--- a/MRMTransitionGroupPicker.xml	Fri Nov 06 20:40:03 2020 +0000
+++ b/MRMTransitionGroupPicker.xml	Thu Dec 01 19:11:36 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="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Picks peaks in SRM/MRM chromatograms.</description>
   <macros>
     <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -45,22 +43,22 @@
     <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="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
+    <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
       <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
-      <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
-      <param name="peak_integration" argument="-algorithm:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
+      <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" optional="true" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
+      <param name="peak_integration" argument="-algorithm:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
         <option value="original" selected="true">original</option>
         <option value="smoothed">smoothed</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="peak_integration"/>
       </param>
-      <param name="background_subtraction" argument="-algorithm:background_subtraction" display="radio" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
+      <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" optional="true" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
         <option value="none" selected="true">none</option>
         <option value="original">original</option>
         <option value="exact">exact</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="background_subtraction"/>
       </param>
       <param name="recalculate_peaks" argument="-algorithm:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
       <param name="use_precursors" argument="-algorithm:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
@@ -71,10 +69,10 @@
       <param name="compute_peak_quality" argument="-algorithm:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
       <param name="compute_peak_shape_metrics" argument="-algorithm:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
       <param name="compute_total_mi" argument="-algorithm:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
-      <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
+      <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help="">
         <option value="largest" selected="true">largest</option>
         <option value="widest">widest</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="boundary_selection_method"/>
       </param>
       <section name="PeakPickerMRM" title="" help="" expanded="false">
         <param name="sgolay_frame_length" argument="-algorithm:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
@@ -87,34 +85,34 @@
         <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/>
         <param name="write_sn_log_messages" argument="-algorithm:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
         <param name="remove_overlapping_peaks" argument="-algorithm:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
-        <param name="method" argument="-algorithm:PeakPickerMRM:method" display="radio" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
+        <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" optional="true" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
           <option value="legacy">legacy</option>
           <option value="corrected" selected="true">corrected</option>
           <option value="crawdad">crawdad</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="method"/>
         </param>
       </section>
       <section name="PeakIntegrator" title="" help="" expanded="false">
-        <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" display="radio" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
+        <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" optional="true" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
           <option value="intensity_sum" selected="true">intensity_sum</option>
           <option value="simpson">simpson</option>
           <option value="trapezoid">trapezoid</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="integration_type"/>
         </param>
-        <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" display="radio" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
+        <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" optional="true" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
           <option value="base_to_base" selected="true">base_to_base</option>
           <option value="vertical_division">vertical_division</option>
           <option value="vertical_division_min">vertical_division_min</option>
           <option value="vertical_division_max">vertical_division_max</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="baseline_type"/>
         </param>
         <param name="fit_EMG" argument="-algorithm:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/>
       </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">
@@ -127,13 +125,112 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MRMTransitionGroupPicker"/>
-    <expand macro="manutest_MRMTransitionGroupPicker"/>
+  <tests><!-- UTILS_MRMTransitionGroupPicker_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="MRMTransitionGroupPicker_1_input.mzML"/>
+      <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
+      <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <section name="algorithm">
+        <param name="stop_after_feature" value="-1"/>
+        <param name="stop_after_intensity_ratio" value="0.0001"/>
+        <param name="min_peak_width" value="0.001"/>
+        <param name="peak_integration" value="original"/>
+        <param name="background_subtraction" value="none"/>
+        <param name="recalculate_peaks" value="false"/>
+        <param name="use_precursors" value="false"/>
+        <param name="use_consensus" value="true"/>
+        <param name="recalculate_peaks_max_z" value="1.0"/>
+        <param name="minimal_quality" value="-10000.0"/>
+        <param name="resample_boundary" value="15.0"/>
+        <param name="compute_peak_quality" value="false"/>
+        <param name="compute_peak_shape_metrics" value="false"/>
+        <param name="compute_total_mi" value="false"/>
+        <param name="boundary_selection_method" value="largest"/>
+        <section name="PeakPickerMRM">
+          <param name="sgolay_frame_length" value="15"/>
+          <param name="sgolay_polynomial_order" value="3"/>
+          <param name="gauss_width" value="50.0"/>
+          <param name="use_gauss" value="true"/>
+          <param name="peak_width" value="40.0"/>
+          <param name="signal_to_noise" value="1.0"/>
+          <param name="sn_win_len" value="1000.0"/>
+          <param name="sn_bin_count" value="30"/>
+          <param name="write_sn_log_messages" value="false"/>
+          <param name="remove_overlapping_peaks" value="true"/>
+          <param name="method" value="legacy"/>
+        </section>
+        <section name="PeakIntegrator">
+          <param name="integration_type" value="intensity_sum"/>
+          <param name="baseline_type" value="base_to_base"/>
+          <param name="fit_EMG" value="false"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- UTILS_MRMTransitionGroupPicker_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="MRMTransitionGroupPicker_1_input.mzML"/>
+      <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
+      <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <section name="algorithm">
+        <param name="stop_after_feature" value="-1"/>
+        <param name="stop_after_intensity_ratio" value="0.0001"/>
+        <param name="min_peak_width" value="0.001"/>
+        <param name="peak_integration" value="original"/>
+        <param name="background_subtraction" value="none"/>
+        <param name="recalculate_peaks" value="false"/>
+        <param name="use_precursors" value="false"/>
+        <param name="use_consensus" value="true"/>
+        <param name="recalculate_peaks_max_z" value="1.0"/>
+        <param name="minimal_quality" value="-10000.0"/>
+        <param name="resample_boundary" value="15.0"/>
+        <param name="compute_peak_quality" value="false"/>
+        <param name="compute_peak_shape_metrics" value="false"/>
+        <param name="compute_total_mi" value="true"/>
+        <param name="boundary_selection_method" value="largest"/>
+        <section name="PeakPickerMRM">
+          <param name="sgolay_frame_length" value="15"/>
+          <param name="sgolay_polynomial_order" value="3"/>
+          <param name="gauss_width" value="50.0"/>
+          <param name="use_gauss" value="true"/>
+          <param name="peak_width" value="40.0"/>
+          <param name="signal_to_noise" value="1.0"/>
+          <param name="sn_win_len" value="1000.0"/>
+          <param name="sn_bin_count" value="30"/>
+          <param name="write_sn_log_messages" value="false"/>
+          <param name="remove_overlapping_peaks" value="true"/>
+          <param name="method" value="legacy"/>
+        </section>
+        <section name="PeakIntegrator">
+          <param name="integration_type" value="intensity_sum"/>
+          <param name="baseline_type" value="base_to_base"/>
+          <param name="fit_EMG" value="false"/>
+        </section>
+      </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[Picks peaks in SRM/MRM chromatograms.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MRMTransitionGroupPicker.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMTransitionGroupPicker.html]]></help>
   <expand macro="references"/>
 </tool>