annotate IsobaricAnalyzer.xml @ 13:130ffca1ec5b draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

<?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: [Quantitation]-->
<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Calculates isobaric quantitative values for peptides</description>
  <macros>
    <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <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 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($in.ext)'
-out
'out/output.${gxy2omsext("consensusxml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("consensusxml")}' '$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 argument="-type" type="select" optional="true" label="Isobaric Quantitation method used in the experiment" help="">
      <option value="itraq4plex" selected="true">itraq4plex</option>
      <option value="itraq8plex">itraq8plex</option>
      <option value="tmt10plex">tmt10plex</option>
      <option value="tmt11plex">tmt11plex</option>
      <option value="tmt16plex">tmt16plex</option>
      <option value="tmt6plex">tmt6plex</option>
      <expand macro="list_string_san" name="type"/>
    </param>
    <param argument="-in" type="data" format="mzml" optional="false" label="input raw/picked data file" help=" select mzml data sets(s)"/>
    <section name="extraction" title="Parameters for the channel extraction" help="" expanded="false">
      <param name="select_activation" argument="-extraction:select_activation" type="select" optional="true" label="Operate only on MSn scans where any of its precursors features a certain activation method" help="Setting to &quot;auto&quot; uses HCD and HCID spectra. Set to empty string if you want to disable filtering">
        <option value="auto" selected="true">auto</option>
        <option value="Collision-induced dissociation">Collision-induced dissociation</option>
        <option value="Post-source decay">Post-source decay</option>
        <option value="Plasma desorption">Plasma desorption</option>
        <option value="Surface-induced dissociation">Surface-induced dissociation</option>
        <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
        <option value="Electron capture dissociation">Electron capture dissociation</option>
        <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
        <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
        <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
        <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
        <option value="Photodissociation">Photodissociation</option>
        <option value="Electron transfer dissociation">Electron transfer dissociation</option>
        <option value="Pulsed q dissociation">Pulsed q dissociation</option>
        <option value="trap-type collision-induced dissociation">trap-type collision-induced dissociation</option>
        <option value="beam-type collision-induced dissociation">beam-type collision-induced dissociation</option>
        <option value="in-source collision-induced dissociation">in-source collision-induced dissociation</option>
        <option value=""></option>
        <expand macro="list_string_san" name="select_activation"/>
      </param>
      <param name="reporter_mass_shift" argument="-extraction:reporter_mass_shift" type="float" optional="true" min="0.0001" max="0.5" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help=""/>
      <param name="min_precursor_intensity" argument="-extraction:min_precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Minimum intensity of the precursor to be extracted" help="MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
      <param name="keep_unannotated_precursor" argument="-extraction:keep_unannotated_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help=""/>
      <param name="min_reporter_intensity" argument="-extraction:min_reporter_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help=""/>
      <param name="discard_low_intensity_quantifications" argument="-extraction:discard_low_intensity_quantifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help=""/>
      <param name="min_precursor_purity" argument="-extraction:min_precursor_purity" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help=""/>
      <param name="precursor_isotope_deviation" argument="-extraction:precursor_isotope_deviation" type="float" optional="true" min="0.0" value="10.0" label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" help=""/>
      <param name="purity_interpolation" argument="-extraction:purity_interpolation" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan" help="If set to false, only the precursor scan will be used"/>
    </section>
    <section name="itraq4plex" title="Algorithm parameters for iTRAQ 4-plex" help="" expanded="false">
      <param name="channel_114_description" argument="-itraq4plex:channel_114_description" type="text" optional="true" value="" label="Description for the content of the 114 channel" help="">
        <expand macro="list_string_san" name="channel_114_description"/>
      </param>
      <param name="channel_115_description" argument="-itraq4plex:channel_115_description" type="text" optional="true" value="" label="Description for the content of the 115 channel" help="">
        <expand macro="list_string_san" name="channel_115_description"/>
      </param>
      <param name="channel_116_description" argument="-itraq4plex:channel_116_description" type="text" optional="true" value="" label="Description for the content of the 116 channel" help="">
        <expand macro="list_string_san" name="channel_116_description"/>
      </param>
      <param name="channel_117_description" argument="-itraq4plex:channel_117_description" type="text" optional="true" value="" label="Description for the content of the 117 channel" help="">
        <expand macro="list_string_san" name="channel_117_description"/>
      </param>
      <param name="reference_channel" argument="-itraq4plex:reference_channel" type="integer" optional="true" min="114" max="117" value="114" label="Number of the reference channel (114-117)" help=""/>
      <param name="correction_matrix" argument="-itraq4plex:correction_matrix" type="text" optional="true" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_string_val" name="correction_matrix"/>
        <expand macro="list_string_san" name="correction_matrix"/>
      </param>
    </section>
    <section name="itraq8plex" title="Algorithm parameters for iTRAQ 8-plex" help="" expanded="false">
      <param name="channel_113_description" argument="-itraq8plex:channel_113_description" type="text" optional="true" value="" label="Description for the content of the 113 channel" help="">
        <expand macro="list_string_san" name="channel_113_description"/>
      </param>
      <param name="channel_114_description" argument="-itraq8plex:channel_114_description" type="text" optional="true" value="" label="Description for the content of the 114 channel" help="">
        <expand macro="list_string_san" name="channel_114_description"/>
      </param>
      <param name="channel_115_description" argument="-itraq8plex:channel_115_description" type="text" optional="true" value="" label="Description for the content of the 115 channel" help="">
        <expand macro="list_string_san" name="channel_115_description"/>
      </param>
      <param name="channel_116_description" argument="-itraq8plex:channel_116_description" type="text" optional="true" value="" label="Description for the content of the 116 channel" help="">
        <expand macro="list_string_san" name="channel_116_description"/>
      </param>
      <param name="channel_117_description" argument="-itraq8plex:channel_117_description" type="text" optional="true" value="" label="Description for the content of the 117 channel" help="">
        <expand macro="list_string_san" name="channel_117_description"/>
      </param>
      <param name="channel_118_description" argument="-itraq8plex:channel_118_description" type="text" optional="true" value="" label="Description for the content of the 118 channel" help="">
        <expand macro="list_string_san" name="channel_118_description"/>
      </param>
      <param name="channel_119_description" argument="-itraq8plex:channel_119_description" type="text" optional="true" value="" label="Description for the content of the 119 channel" help="">
        <expand macro="list_string_san" name="channel_119_description"/>
      </param>
      <param name="channel_121_description" argument="-itraq8plex:channel_121_description" type="text" optional="true" value="" label="Description for the content of the 121 channel" help="">
        <expand macro="list_string_san" name="channel_121_description"/>
      </param>
      <param name="reference_channel" argument="-itraq8plex:reference_channel" type="integer" optional="true" min="113" max="121" value="113" label="Number of the reference channel (113-121)" help="Please note that 120 is not valid"/>
      <param name="correction_matrix" argument="-itraq8plex:correction_matrix" type="text" optional="true" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_string_val" name="correction_matrix"/>
        <expand macro="list_string_san" name="correction_matrix"/>
      </param>
    </section>
    <section name="quantification" title="Parameters for the peptide quantification" help="" expanded="false">
      <param name="isotope_correction" argument="-quantification:isotope_correction" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable isotope correction (highly recommended)" help="Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results"/>
      <param name="normalization" argument="-quantification:normalization" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable normalization of channel intensities with respect to the reference channel" help="The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/>
    </section>
    <section name="tmt10plex" title="Algorithm parameters for TMT 10-plex" help="" expanded="false">
      <param name="channel_126_description" argument="-tmt10plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help="">
        <expand macro="list_string_san" name="channel_126_description"/>
      </param>
      <param name="channel_127N_description" argument="-tmt10plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help="">
        <expand macro="list_string_san" name="channel_127N_description"/>
      </param>
      <param name="channel_127C_description" argument="-tmt10plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help="">
        <expand macro="list_string_san" name="channel_127C_description"/>
      </param>
      <param name="channel_128N_description" argument="-tmt10plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help="">
        <expand macro="list_string_san" name="channel_128N_description"/>
      </param>
      <param name="channel_128C_description" argument="-tmt10plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help="">
        <expand macro="list_string_san" name="channel_128C_description"/>
      </param>
      <param name="channel_129N_description" argument="-tmt10plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help="">
        <expand macro="list_string_san" name="channel_129N_description"/>
      </param>
      <param name="channel_129C_description" argument="-tmt10plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help="">
        <expand macro="list_string_san" name="channel_129C_description"/>
      </param>
      <param name="channel_130N_description" argument="-tmt10plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help="">
        <expand macro="list_string_san" name="channel_130N_description"/>
      </param>
      <param name="channel_130C_description" argument="-tmt10plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help="">
        <expand macro="list_string_san" name="channel_130C_description"/>
      </param>
      <param name="channel_131_description" argument="-tmt10plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help="">
        <expand macro="list_string_san" name="channel_131_description"/>
      </param>
      <param name="reference_channel" argument="-tmt10plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="">
        <option value="126" selected="true">126</option>
        <option value="127N">127N</option>
        <option value="127C">127C</option>
        <option value="128N">128N</option>
        <option value="128C">128C</option>
        <option value="129N">129N</option>
        <option value="129C">129C</option>
        <option value="130N">130N</option>
        <option value="130C">130C</option>
        <option value="131">131</option>
        <expand macro="list_string_san" name="reference_channel"/>
      </param>
      <param name="correction_matrix" argument="-tmt10plex:correction_matrix" type="text" optional="true" value="0.0/0.0/5.09/0.0 0.0/0.25/5.27/0.0 0.0/0.37/5.36/0.15 0.0/0.65/4.17/0.1 0.08/0.49/3.06/0.0 0.01/0.71/3.07/0.0 0.0/1.32/2.62/0.0 0.02/1.28/2.75/2.53 0.03/2.08/2.23/0.0 0.08/1.99/1.65/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_string_val" name="correction_matrix"/>
        <expand macro="list_string_san" name="correction_matrix"/>
      </param>
    </section>
    <section name="tmt11plex" title="Algorithm parameters for TMT 11-plex" help="" expanded="false">
      <param name="channel_126_description" argument="-tmt11plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help="">
        <expand macro="list_string_san" name="channel_126_description"/>
      </param>
      <param name="channel_127N_description" argument="-tmt11plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help="">
        <expand macro="list_string_san" name="channel_127N_description"/>
      </param>
      <param name="channel_127C_description" argument="-tmt11plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help="">
        <expand macro="list_string_san" name="channel_127C_description"/>
      </param>
      <param name="channel_128N_description" argument="-tmt11plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help="">
        <expand macro="list_string_san" name="channel_128N_description"/>
      </param>
      <param name="channel_128C_description" argument="-tmt11plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help="">
        <expand macro="list_string_san" name="channel_128C_description"/>
      </param>
      <param name="channel_129N_description" argument="-tmt11plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help="">
        <expand macro="list_string_san" name="channel_129N_description"/>
      </param>
      <param name="channel_129C_description" argument="-tmt11plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help="">
        <expand macro="list_string_san" name="channel_129C_description"/>
      </param>
      <param name="channel_130N_description" argument="-tmt11plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help="">
        <expand macro="list_string_san" name="channel_130N_description"/>
      </param>
      <param name="channel_130C_description" argument="-tmt11plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help="">
        <expand macro="list_string_san" name="channel_130C_description"/>
      </param>
      <param name="channel_131N_description" argument="-tmt11plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help="">
        <expand macro="list_string_san" name="channel_131N_description"/>
      </param>
      <param name="channel_131C_description" argument="-tmt11plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help="">
        <expand macro="list_string_san" name="channel_131C_description"/>
      </param>
      <param name="reference_channel" argument="-tmt11plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="">
        <option value="126" selected="true">126</option>
        <option value="127N">127N</option>
        <option value="127C">127C</option>
        <option value="128N">128N</option>
        <option value="128C">128C</option>
        <option value="129N">129N</option>
        <option value="129C">129C</option>
        <option value="130N">130N</option>
        <option value="130C">130C</option>
        <option value="131N">131N</option>
        <option value="131C">131C</option>
        <expand macro="list_string_san" name="reference_channel"/>
      </param>
      <param name="correction_matrix" argument="-tmt11plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_string_val" name="correction_matrix"/>
        <expand macro="list_string_san" name="correction_matrix"/>
      </param>
    </section>
    <section name="tmt16plex" title="Algorithm parameters for TMT 16-plex" help="" expanded="false">
      <param name="channel_126_description" argument="-tmt16plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help="">
        <expand macro="list_string_san" name="channel_126_description"/>
      </param>
      <param name="channel_127N_description" argument="-tmt16plex:channel_127N_description" type="text" optional="true" value="" label="Description for the content of the 127N channel" help="">
        <expand macro="list_string_san" name="channel_127N_description"/>
      </param>
      <param name="channel_127C_description" argument="-tmt16plex:channel_127C_description" type="text" optional="true" value="" label="Description for the content of the 127C channel" help="">
        <expand macro="list_string_san" name="channel_127C_description"/>
      </param>
      <param name="channel_128N_description" argument="-tmt16plex:channel_128N_description" type="text" optional="true" value="" label="Description for the content of the 128N channel" help="">
        <expand macro="list_string_san" name="channel_128N_description"/>
      </param>
      <param name="channel_128C_description" argument="-tmt16plex:channel_128C_description" type="text" optional="true" value="" label="Description for the content of the 128C channel" help="">
        <expand macro="list_string_san" name="channel_128C_description"/>
      </param>
      <param name="channel_129N_description" argument="-tmt16plex:channel_129N_description" type="text" optional="true" value="" label="Description for the content of the 129N channel" help="">
        <expand macro="list_string_san" name="channel_129N_description"/>
      </param>
      <param name="channel_129C_description" argument="-tmt16plex:channel_129C_description" type="text" optional="true" value="" label="Description for the content of the 129C channel" help="">
        <expand macro="list_string_san" name="channel_129C_description"/>
      </param>
      <param name="channel_130N_description" argument="-tmt16plex:channel_130N_description" type="text" optional="true" value="" label="Description for the content of the 130N channel" help="">
        <expand macro="list_string_san" name="channel_130N_description"/>
      </param>
      <param name="channel_130C_description" argument="-tmt16plex:channel_130C_description" type="text" optional="true" value="" label="Description for the content of the 130C channel" help="">
        <expand macro="list_string_san" name="channel_130C_description"/>
      </param>
      <param name="channel_131N_description" argument="-tmt16plex:channel_131N_description" type="text" optional="true" value="" label="Description for the content of the 131N channel" help="">
        <expand macro="list_string_san" name="channel_131N_description"/>
      </param>
      <param name="channel_131C_description" argument="-tmt16plex:channel_131C_description" type="text" optional="true" value="" label="Description for the content of the 131C channel" help="">
        <expand macro="list_string_san" name="channel_131C_description"/>
      </param>
      <param name="channel_132N_description" argument="-tmt16plex:channel_132N_description" type="text" optional="true" value="" label="Description for the content of the 132N channel" help="">
        <expand macro="list_string_san" name="channel_132N_description"/>
      </param>
      <param name="channel_132C_description" argument="-tmt16plex:channel_132C_description" type="text" optional="true" value="" label="Description for the content of the 132C channel" help="">
        <expand macro="list_string_san" name="channel_132C_description"/>
      </param>
      <param name="channel_133N_description" argument="-tmt16plex:channel_133N_description" type="text" optional="true" value="" label="Description for the content of the 133N channel" help="">
        <expand macro="list_string_san" name="channel_133N_description"/>
      </param>
      <param name="channel_133C_description" argument="-tmt16plex:channel_133C_description" type="text" optional="true" value="" label="Description for the content of the 133C channel" help="">
        <expand macro="list_string_san" name="channel_133C_description"/>
      </param>
      <param name="channel_134N_description" argument="-tmt16plex:channel_134N_description" type="text" optional="true" value="" label="Description for the content of the 134N channel" help="">
        <expand macro="list_string_san" name="channel_134N_description"/>
      </param>
      <param name="reference_channel" argument="-tmt16plex:reference_channel" type="select" optional="true" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="">
        <option value="126" selected="true">126</option>
        <option value="127N">127N</option>
        <option value="127C">127C</option>
        <option value="128N">128N</option>
        <option value="128C">128C</option>
        <option value="129N">129N</option>
        <option value="129C">129C</option>
        <option value="130N">130N</option>
        <option value="130C">130C</option>
        <option value="131N">131N</option>
        <option value="131C">131C</option>
        <option value="132N">132N</option>
        <option value="132C">132C</option>
        <option value="133N">133N</option>
        <option value="133C">133C</option>
        <option value="134N">134N</option>
        <expand macro="list_string_san" name="reference_channel"/>
      </param>
      <param name="correction_matrix" argument="-tmt16plex:correction_matrix" type="text" optional="true" value="0.0/0.0/8.02/0.0 0.0/0.68/7.46/0.0 0.0/0.71/6.94/0.0 0.0/1.88/6.67/0.0 0.0/1.34/5.59/0.0 0.0/2.41/5.48/0.0 0.0/2.34/5.19/0.0 0.0/3.53/4.57/0.0 0.0/2.67/4.16/0.0 0.0/3.92/3.73/0.0 0.0/3.69/3.14/0.0 0.0/3.22/2.76/0.0 0.0/4.11/2.0/0.0 0.0/3.85/1.58/0.0 0.0/4.63/1.18/0.0 0.0/5.22/0.86/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_string_val" name="correction_matrix"/>
        <expand macro="list_string_san" name="correction_matrix"/>
      </param>
    </section>
    <section name="tmt6plex" title="Algorithm parameters for TMT 6-plex" help="" expanded="false">
      <param name="channel_126_description" argument="-tmt6plex:channel_126_description" type="text" optional="true" value="" label="Description for the content of the 126 channel" help="">
        <expand macro="list_string_san" name="channel_126_description"/>
      </param>
      <param name="channel_127_description" argument="-tmt6plex:channel_127_description" type="text" optional="true" value="" label="Description for the content of the 127 channel" help="">
        <expand macro="list_string_san" name="channel_127_description"/>
      </param>
      <param name="channel_128_description" argument="-tmt6plex:channel_128_description" type="text" optional="true" value="" label="Description for the content of the 128 channel" help="">
        <expand macro="list_string_san" name="channel_128_description"/>
      </param>
      <param name="channel_129_description" argument="-tmt6plex:channel_129_description" type="text" optional="true" value="" label="Description for the content of the 129 channel" help="">
        <expand macro="list_string_san" name="channel_129_description"/>
      </param>
      <param name="channel_130_description" argument="-tmt6plex:channel_130_description" type="text" optional="true" value="" label="Description for the content of the 130 channel" help="">
        <expand macro="list_string_san" name="channel_130_description"/>
      </param>
      <param name="channel_131_description" argument="-tmt6plex:channel_131_description" type="text" optional="true" value="" label="Description for the content of the 131 channel" help="">
        <expand macro="list_string_san" name="channel_131_description"/>
      </param>
      <param name="reference_channel" argument="-tmt6plex:reference_channel" type="integer" optional="true" min="126" max="131" value="126" label="Number of the reference channel (126-131)" help=""/>
      <param name="correction_matrix" argument="-tmt6plex:correction_matrix" type="text" optional="true" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="e.g. '0/0.3/4/0', '0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_string_val" name="correction_matrix"/>
        <expand macro="list_string_san" name="correction_matrix"/>
      </param>
    </section>
    <expand macro="adv_opts_macro">
      <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">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><!-- TOPP_IsobaricAnalyzer_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="type" value="itraq4plex"/>
      <param name="in" value="IsobaricAnalyzer_input_1.mzML"/>
      <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <section name="extraction">
        <param name="select_activation"/>
        <param name="reporter_mass_shift" value="0.1"/>
        <param name="min_precursor_intensity" value="1.0"/>
        <param name="keep_unannotated_precursor" value="true"/>
        <param name="min_reporter_intensity" value="0.0"/>
        <param name="discard_low_intensity_quantifications" value="false"/>
        <param name="min_precursor_purity" value="0.0"/>
        <param name="precursor_isotope_deviation" value="10.0"/>
        <param name="purity_interpolation" value="true"/>
      </section>
      <section name="itraq4plex">
        <param name="channel_114_description" value="l1"/>
        <param name="channel_115_description" value="l2"/>
        <param name="channel_116_description" value="l3"/>
        <param name="channel_117_description" value="lung"/>
        <param name="reference_channel" value="114"/>
        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
      </section>
      <section name="itraq8plex">
        <param name="channel_113_description" value=""/>
        <param name="channel_114_description" value=""/>
        <param name="channel_115_description" value=""/>
        <param name="channel_116_description" value=""/>
        <param name="channel_117_description" value=""/>
        <param name="channel_118_description" value=""/>
        <param name="channel_119_description" value=""/>
        <param name="channel_121_description" value=""/>
        <param name="reference_channel" value="113"/>
        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
      </section>
      <section name="quantification">
        <param name="isotope_correction" value="true"/>
        <param name="normalization" value="false"/>
      </section>
      <section name="tmt10plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </section>
      <section name="tmt11plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </section>
      <section name="tmt16plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="channel_132N_description" value=""/>
        <param name="channel_132C_description" value=""/>
        <param name="channel_133N_description" value=""/>
        <param name="channel_133C_description" value=""/>
        <param name="channel_134N_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
      </section>
      <section name="tmt6plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127_description" value=""/>
        <param name="channel_128_description" value=""/>
        <param name="channel_129_description" value=""/>
        <param name="channel_130_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </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_IsobaricAnalyzer_TMTTenPlexMethod_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="type" value="itraq4plex"/>
      <param name="in" value="TMTTenPlexMethod_test.mzML"/>
      <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <section name="extraction">
        <param name="select_activation" value="auto"/>
        <param name="reporter_mass_shift" value="0.002"/>
        <param name="min_precursor_intensity" value="1.0"/>
        <param name="keep_unannotated_precursor" value="true"/>
        <param name="min_reporter_intensity" value="0.0"/>
        <param name="discard_low_intensity_quantifications" value="false"/>
        <param name="min_precursor_purity" value="0.0"/>
        <param name="precursor_isotope_deviation" value="10.0"/>
        <param name="purity_interpolation" value="true"/>
      </section>
      <section name="itraq4plex">
        <param name="channel_114_description" value=""/>
        <param name="channel_115_description" value=""/>
        <param name="channel_116_description" value=""/>
        <param name="channel_117_description" value=""/>
        <param name="reference_channel" value="114"/>
        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
      </section>
      <section name="itraq8plex">
        <param name="channel_113_description" value=""/>
        <param name="channel_114_description" value=""/>
        <param name="channel_115_description" value=""/>
        <param name="channel_116_description" value=""/>
        <param name="channel_117_description" value=""/>
        <param name="channel_118_description" value=""/>
        <param name="channel_119_description" value=""/>
        <param name="channel_121_description" value=""/>
        <param name="reference_channel" value="113"/>
        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
      </section>
      <section name="quantification">
        <param name="isotope_correction" value="true"/>
        <param name="normalization" value="false"/>
      </section>
      <section name="tmt10plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/5.0/0.0&quot; &quot;0.0/0.2/4.6/0.0&quot; &quot;0.0/0.2/4.6/0.3&quot; &quot;0.0/0.9/4.7/0.2&quot; &quot;0.0/0.5/3.2/0.0&quot; &quot;0.0/0.7/3.3/0.0&quot; &quot;0.0/1.3/2.5/0.0&quot; &quot;0.0/1.2/2.8/2.7&quot; &quot;0.0/1.5/2.0/0.0&quot; &quot;0.0/1.5/1.9/0.0&quot;"/>
      </section>
      <section name="tmt11plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </section>
      <section name="tmt16plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="channel_132N_description" value=""/>
        <param name="channel_132C_description" value=""/>
        <param name="channel_133N_description" value=""/>
        <param name="channel_133C_description" value=""/>
        <param name="channel_134N_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
      </section>
      <section name="tmt6plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127_description" value=""/>
        <param name="channel_128_description" value=""/>
        <param name="channel_129_description" value=""/>
        <param name="channel_130_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </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_IsobaricAnalyzer_TMTElevenPlexMethod_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="type" value="itraq4plex"/>
      <param name="in" value="TMTTenPlexMethod_test.mzML"/>
      <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <section name="extraction">
        <param name="select_activation" value="auto"/>
        <param name="reporter_mass_shift" value="0.002"/>
        <param name="min_precursor_intensity" value="1.0"/>
        <param name="keep_unannotated_precursor" value="true"/>
        <param name="min_reporter_intensity" value="0.0"/>
        <param name="discard_low_intensity_quantifications" value="false"/>
        <param name="min_precursor_purity" value="0.0"/>
        <param name="precursor_isotope_deviation" value="10.0"/>
        <param name="purity_interpolation" value="true"/>
      </section>
      <section name="itraq4plex">
        <param name="channel_114_description" value=""/>
        <param name="channel_115_description" value=""/>
        <param name="channel_116_description" value=""/>
        <param name="channel_117_description" value=""/>
        <param name="reference_channel" value="114"/>
        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
      </section>
      <section name="itraq8plex">
        <param name="channel_113_description" value=""/>
        <param name="channel_114_description" value=""/>
        <param name="channel_115_description" value=""/>
        <param name="channel_116_description" value=""/>
        <param name="channel_117_description" value=""/>
        <param name="channel_118_description" value=""/>
        <param name="channel_119_description" value=""/>
        <param name="channel_121_description" value=""/>
        <param name="reference_channel" value="113"/>
        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
      </section>
      <section name="quantification">
        <param name="isotope_correction" value="true"/>
        <param name="normalization" value="false"/>
      </section>
      <section name="tmt10plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </section>
      <section name="tmt11plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </section>
      <section name="tmt16plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="channel_132N_description" value=""/>
        <param name="channel_132C_description" value=""/>
        <param name="channel_133N_description" value=""/>
        <param name="channel_133C_description" value=""/>
        <param name="channel_134N_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
      </section>
      <section name="tmt6plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127_description" value=""/>
        <param name="channel_128_description" value=""/>
        <param name="channel_129_description" value=""/>
        <param name="channel_130_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </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_IsobaricAnalyzer_MS3TMT10Plex_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="type" value="tmt10plex"/>
      <param name="in" value="MS3_nonHierarchical.mzML"/>
      <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <section name="extraction">
        <param name="select_activation" value="Collision-induced dissociation"/>
        <param name="reporter_mass_shift" value="0.002"/>
        <param name="min_precursor_intensity" value="1.0"/>
        <param name="keep_unannotated_precursor" value="true"/>
        <param name="min_reporter_intensity" value="0.0"/>
        <param name="discard_low_intensity_quantifications" value="false"/>
        <param name="min_precursor_purity" value="0.0"/>
        <param name="precursor_isotope_deviation" value="10.0"/>
        <param name="purity_interpolation" value="true"/>
      </section>
      <section name="itraq4plex">
        <param name="channel_114_description" value=""/>
        <param name="channel_115_description" value=""/>
        <param name="channel_116_description" value=""/>
        <param name="channel_117_description" value=""/>
        <param name="reference_channel" value="114"/>
        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
      </section>
      <section name="itraq8plex">
        <param name="channel_113_description" value=""/>
        <param name="channel_114_description" value=""/>
        <param name="channel_115_description" value=""/>
        <param name="channel_116_description" value=""/>
        <param name="channel_117_description" value=""/>
        <param name="channel_118_description" value=""/>
        <param name="channel_119_description" value=""/>
        <param name="channel_121_description" value=""/>
        <param name="reference_channel" value="113"/>
        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
      </section>
      <section name="quantification">
        <param name="isotope_correction" value="true"/>
        <param name="normalization" value="false"/>
      </section>
      <section name="tmt10plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/5.09/0.0&quot; &quot;0.0/0.25/5.27/0.0&quot; &quot;0.0/0.37/5.36/0.15&quot; &quot;0.0/0.65/4.17/0.1&quot; &quot;0.08/0.49/3.06/0.0&quot; &quot;0.01/0.71/3.07/0.0&quot; &quot;0.0/1.32/2.62/0.0&quot; &quot;0.02/1.28/2.75/2.53&quot; &quot;0.03/2.08/2.23/0.0&quot; &quot;0.08/1.99/1.65/0.0&quot;"/>
      </section>
      <section name="tmt11plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </section>
      <section name="tmt16plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127N_description" value=""/>
        <param name="channel_127C_description" value=""/>
        <param name="channel_128N_description" value=""/>
        <param name="channel_128C_description" value=""/>
        <param name="channel_129N_description" value=""/>
        <param name="channel_129C_description" value=""/>
        <param name="channel_130N_description" value=""/>
        <param name="channel_130C_description" value=""/>
        <param name="channel_131N_description" value=""/>
        <param name="channel_131C_description" value=""/>
        <param name="channel_132N_description" value=""/>
        <param name="channel_132C_description" value=""/>
        <param name="channel_133N_description" value=""/>
        <param name="channel_133C_description" value=""/>
        <param name="channel_134N_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
      </section>
      <section name="tmt6plex">
        <param name="channel_126_description" value=""/>
        <param name="channel_127_description" value=""/>
        <param name="channel_128_description" value=""/>
        <param name="channel_129_description" value=""/>
        <param name="channel_130_description" value=""/>
        <param name="channel_131_description" value=""/>
        <param name="reference_channel" value="126"/>
        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
      </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[Calculates isobaric quantitative values for peptides


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IsobaricAnalyzer.html]]></help>
  <expand macro="references"/>
</tool>