--- a/MetaProSIP.xml	Fri Nov 06 20:29:40 2020 +0000
+++ b/MetaProSIP.xml	Thu Dec 01 18:58:27 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="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaProSIP</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -53,56 +51,56 @@
     <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in_mzML" argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
-    <param name="in_fasta" argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/>
-    <param name="in_featureXML" argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
-    <param name="mz_tolerance_ppm" argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/>
-    <param name="rt_tolerance_s" argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/>
-    <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
-    <param name="correlation_threshold" argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
-    <param name="xic_threshold" argument="-xic_threshold" type="float" optional="true" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
-    <param name="decomposition_threshold" argument="-decomposition_threshold" type="float" optional="true" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
-    <param name="weight_merge_window" argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
-    <param name="plot_extension" argument="-plot_extension" display="radio" type="select" optional="false" label="Extension used for plots (png|svg|pdf)" help="">
+    <param argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
+    <param argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/>
+    <param argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
+    <param argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/>
+    <param argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/>
+    <param argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
+    <param argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
+    <param argument="-xic_threshold" type="float" optional="true" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
+    <param argument="-decomposition_threshold" type="float" optional="true" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
+    <param argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
+    <param argument="-plot_extension" type="select" optional="true" label="Extension used for plots (png|svg|pdf)" help="">
       <option value="png" selected="true">png</option>
       <option value="svg">svg</option>
       <option value="pdf">pdf</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="plot_extension"/>
     </param>
-    <param name="qc_output_directory" argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
+      <expand macro="list_string_san" name="qc_output_directory"/>
     </param>
-    <param name="labeling_element" argument="-labeling_element" display="radio" type="select" optional="false" label="Which element (single letter code) is labeled" help="">
+    <param argument="-labeling_element" type="select" optional="true" label="Which element (single letter code) is labeled" help="">
       <option value="C" selected="true">C</option>
       <option value="N">N</option>
       <option value="H">H</option>
       <option value="O">O</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="labeling_element"/>
     </param>
-    <param name="use_unassigned_ids" argument="-use_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include identifications not assigned to a feature in pattern detection" help=""/>
-    <param name="use_averagine_ids" argument="-use_averagine_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help=""/>
-    <param name="report_natural_peptides" argument="-report_natural_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether purely natural peptides are reported in the quality report" help=""/>
-    <param name="filter_monoisotopic" argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/>
-    <param name="cluster" argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/>
+    <param argument="-use_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include identifications not assigned to a feature in pattern detection" help=""/>
+    <param argument="-use_averagine_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help=""/>
+    <param argument="-report_natural_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether purely natural peptides are reported in the quality report" help=""/>
+    <param argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/>
+    <param argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/>
     <expand macro="adv_opts_macro">
-      <param name="min_correlation_distance_to_averagine" argument="-min_correlation_distance_to_averagine" type="float" optional="true" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
-      <param name="pattern_15N_TIC_threshold" argument="-pattern_15N_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param name="pattern_13C_TIC_threshold" argument="-pattern_13C_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param name="pattern_2H_TIC_threshold" argument="-pattern_2H_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param name="pattern_18O_TIC_threshold" argument="-pattern_18O_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param name="heatmap_bins" argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/>
-      <param name="observed_peak_fraction" argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/>
-      <param name="min_consecutive_isotopes" argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
-      <param name="score_plot_yaxis_min" argument="-score_plot_yaxis_min" type="float" optional="true" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
-      <param name="collect_method" argument="-collect_method" display="radio" type="select" optional="false" label="How RIAs are collected" help="">
+      <param argument="-min_correlation_distance_to_averagine" type="float" optional="true" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
+      <param argument="-pattern_15N_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_13C_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_2H_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_18O_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/>
+      <param argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/>
+      <param argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
+      <param argument="-score_plot_yaxis_min" type="float" optional="true" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
+      <param argument="-collect_method" type="select" optional="true" label="How RIAs are collected" help="">
         <option value="correlation_maximum" selected="true">correlation_maximum</option>
         <option value="decomposition_maximum">decomposition_maximum</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="collect_method"/>
       </param>
-      <param name="lowRIA_correlation_threshold" argument="-lowRIA_correlation_threshold" type="float" optional="true" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
-      <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="-lowRIA_correlation_threshold" type="float" optional="true" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
+      <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">
@@ -116,13 +114,54 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MetaProSIP"/>
-    <expand macro="manutest_MetaProSIP"/>
+  <tests><!-- TOPP_MetaProSIP_1 -->
+    <test expect_num_outputs="3">
+      <section name="adv_opts">
+        <param name="min_correlation_distance_to_averagine" value="-1.0"/>
+        <param name="pattern_15N_TIC_threshold" value="0.95"/>
+        <param name="pattern_13C_TIC_threshold" value="0.95"/>
+        <param name="pattern_2H_TIC_threshold" value="0.95"/>
+        <param name="pattern_18O_TIC_threshold" value="0.95"/>
+        <param name="heatmap_bins" value="20"/>
+        <param name="observed_peak_fraction" value="0.5"/>
+        <param name="min_consecutive_isotopes" value="2"/>
+        <param name="score_plot_yaxis_min" value="0.0"/>
+        <param name="collect_method" value="correlation_maximum"/>
+        <param name="lowRIA_correlation_threshold" value="-1.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
+      <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
+      <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
+      <param name="mz_tolerance_ppm" value="10.0"/>
+      <param name="rt_tolerance_s" value="30.0"/>
+      <param name="intensity_threshold" value="10.0"/>
+      <param name="correlation_threshold" value="0.7"/>
+      <param name="xic_threshold" value="0.7"/>
+      <param name="decomposition_threshold" value="0.7"/>
+      <param name="weight_merge_window" value="5.0"/>
+      <param name="plot_extension" value="png"/>
+      <param name="qc_output_directory" value=""/>
+      <param name="labeling_element" value="C"/>
+      <param name="use_unassigned_ids" value="false"/>
+      <param name="use_averagine_ids" value="false"/>
+      <param name="report_natural_peptides" value="false"/>
+      <param name="filter_monoisotopic" value="false"/>
+      <param name="cluster" value="false"/>
+      <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[Performs proteinSIP on peptide features for elemental flux analysis.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaProSIP.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaProSIP.html]]></help>
   <expand macro="references"/>
 </tool>