--- a/MRMTransitionGroupPicker.xml	Fri May 17 09:59:52 2019 -0400
+++ b/MRMTransitionGroupPicker.xml	Wed Sep 09 12:42:24 2020 +0000
@@ -1,162 +1,139 @@
 <?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="2.3.0">
+<tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <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="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[MRMTransitionGroupPicker
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir tr &&
+ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-tr
+'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
+-out
+'out/output.${gxy2omsext("featurexml")}'
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_tr:
-  -tr $param_tr
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_algorithm_stop_after_feature:
-  -algorithm:stop_after_feature $param_algorithm_stop_after_feature
-#end if
-#if $param_algorithm_stop_after_intensity_ratio:
-  -algorithm:stop_after_intensity_ratio $param_algorithm_stop_after_intensity_ratio
-#end if
-#if $param_algorithm_PeakPickerMRM_sgolay_frame_length:
-  -algorithm:PeakPickerMRM:sgolay_frame_length $param_algorithm_PeakPickerMRM_sgolay_frame_length
-#end if
-#if $param_algorithm_PeakPickerMRM_sgolay_polynomial_order:
-  -algorithm:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_PeakPickerMRM_sgolay_polynomial_order
-#end if
-#if $param_algorithm_PeakPickerMRM_gauss_width:
-  -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width
-#end if
-#if $param_algorithm_PeakPickerMRM_use_gauss:
-  -algorithm:PeakPickerMRM:use_gauss
-  #if " " in str($param_algorithm_PeakPickerMRM_use_gauss):
-    "$param_algorithm_PeakPickerMRM_use_gauss"
-  #else
-    $param_algorithm_PeakPickerMRM_use_gauss
-  #end if
-#end if
-#if $param_algorithm_PeakPickerMRM_peak_width:
-  -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width
-#end if
-#if $param_algorithm_PeakPickerMRM_signal_to_noise:
-  -algorithm:PeakPickerMRM:signal_to_noise $param_algorithm_PeakPickerMRM_signal_to_noise
-#end if
-#if $param_algorithm_PeakPickerMRM_sn_win_len:
-  -algorithm:PeakPickerMRM:sn_win_len $param_algorithm_PeakPickerMRM_sn_win_len
-#end if
-#if $param_algorithm_PeakPickerMRM_sn_bin_count:
-  -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count
-#end if
-#if $param_algorithm_PeakPickerMRM_write_sn_log_messages:
-  -algorithm:PeakPickerMRM:write_sn_log_messages
-  #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages):
-    "$param_algorithm_PeakPickerMRM_write_sn_log_messages"
-  #else
-    $param_algorithm_PeakPickerMRM_write_sn_log_messages
-  #end if
-#end if
-#if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks:
-  -algorithm:PeakPickerMRM:remove_overlapping_peaks
-#end if
-#if $param_algorithm_PeakPickerMRM_method:
-  -algorithm:PeakPickerMRM:method
-  #if " " in str($param_algorithm_PeakPickerMRM_method):
-    "$param_algorithm_PeakPickerMRM_method"
-  #else
-    $param_algorithm_PeakPickerMRM_method
-  #end if
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-    #if $adv_opts.param_algorithm_min_peak_width:
-  -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width
-#end if
-    #if $adv_opts.param_algorithm_background_subtraction:
-  -algorithm:background_subtraction
-  #if " " in str($adv_opts.param_algorithm_background_subtraction):
-    "$adv_opts.param_algorithm_background_subtraction"
-  #else
-    $adv_opts.param_algorithm_background_subtraction
-  #end if
-#end if
-    #if $adv_opts.param_algorithm_recalculate_peaks:
-  -algorithm:recalculate_peaks
-#end if
-    #if $adv_opts.param_algorithm_use_precursors:
-  -algorithm:use_precursors
-#end if
-    #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
-  -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z
-#end if
-    #if $adv_opts.param_algorithm_minimal_quality:
-  -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
-#end if
-    #if $adv_opts.param_algorithm_resample_boundary:
-  -algorithm:resample_boundary $adv_opts.param_algorithm_resample_boundary
-#end if
-    #if $adv_opts.param_algorithm_compute_peak_quality:
-  -algorithm:compute_peak_quality
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("featurexml")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <inputs>
-    <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
-    <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
-    <param name="param_algorithm_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
-    <param name="param_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>
-    <param name="param_algorithm_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
-    <param name="param_algorithm_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
-    <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
-    <param name="param_algorithm_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
-      <option value="false">false</option>
-      <option value="true" selected="true">true</option>
-    </param>
-    <param name="param_algorithm_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
-    <param name="param_algorithm_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
-    <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
-    <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
-    <param name="param_algorithm_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help="(-write_sn_log_messages) ">
-      <option value="true" selected="true">true</option>
-      <option value="false">false</option>
+    <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)"/>
+    <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="">
+        <option value="original" selected="true">original</option>
+        <option value="smoothed">smoothed</option>
+        <expand macro="list_string_san"/>
+      </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">
+        <option value="none" selected="true">none</option>
+        <option value="original">original</option>
+        <option value="exact">exact</option>
+        <expand macro="list_string_san"/>
+      </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=""/>
+      <param name="use_consensus" argument="-algorithm:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
+      <param name="recalculate_peaks_max_z" argument="-algorithm:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
+      <param name="minimal_quality" argument="-algorithm:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
+      <param name="resample_boundary" argument="-algorithm:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
+      <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="">
+        <option value="largest" selected="true">largest</option>
+        <option value="widest">widest</option>
+        <expand macro="list_string_san"/>
+      </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"/>
+        <param name="sgolay_polynomial_order" argument="-algorithm:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
+        <param name="gauss_width" argument="-algorithm:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
+        <param name="use_gauss" argument="-algorithm:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
+        <param name="peak_width" argument="-algorithm:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
+        <param name="signal_to_noise" argument="-algorithm:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
+        <param name="sn_win_len" argument="-algorithm:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/>
+        <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="">
+          <option value="legacy">legacy</option>
+          <option value="corrected" selected="true">corrected</option>
+          <option value="crawdad">crawdad</option>
+          <expand macro="list_string_san"/>
+        </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="">
+          <option value="intensity_sum" selected="true">intensity_sum</option>
+          <option value="simpson">simpson</option>
+          <option value="trapezoid">trapezoid</option>
+          <expand macro="list_string_san"/>
+        </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)">
+          <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"/>
+        </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="Overwrite 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>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
-    <param name="param_algorithm_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
-    <param name="param_algorithm_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" 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="(-method) ">
-      <option value="legacy">legacy</option>
-      <option value="corrected" selected="true">corrected</option>
-      <option value="crawdad">crawdad</option>
-    </param>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
-      <param name="param_algorithm_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
-      <param name="param_algorithm_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
-        <option value="none" selected="true">none</option>
-        <option value="smoothed">smoothed</option>
-        <option value="original">original</option>
-      </param>
-      <param name="param_algorithm_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
-      <param name="param_algorithm_use_precursors" display="radio" type="boolean" truevalue="-algorithm:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
-      <param name="param_algorithm_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
-      <param name="param_algorithm_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
-      <param name="param_algorithm_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>
-      <param name="param_algorithm_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
-    </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="featurexml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Picks peaks in SRM/MRM chromatograms.
+  <tests>
+    <expand macro="autotest_MRMTransitionGroupPicker"/>
+    <expand macro="manutest_MRMTransitionGroupPicker"/>
+  </tests>
+  <help><![CDATA[Picks peaks in SRM/MRM chromatograms.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MRMTransitionGroupPicker.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_MRMTransitionGroupPicker.html]]></help>
+  <expand macro="references"/>
 </tool>