annotate IsobaricAnalyzer.xml @ 1:125774c3e8aa draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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 CTD2Galaxy.-->
<!--Proposed Tool Section: [Quantitation]-->
<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.2.0">
  <description>Calculates isobaric quantitative values for peptides</description>
  <macros>
    <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IsobaricAnalyzer

#if $param_type:
  -type
  #if " " in str($param_type):
    "$param_type"
  #else
    $param_type
  #end if
#end if
#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_id_pool:
  -id_pool     "$param_id_pool"
#end if
#if $param_extraction_select_activation:
  -extraction:select_activation
  #if " " in str($param_extraction_select_activation):
    "$param_extraction_select_activation"
  #else
    $param_extraction_select_activation
  #end if
#end if
#if $param_extraction_reporter_mass_shift:
  -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift
#end if
#if $param_extraction_min_precursor_intensity:
  -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity
#end if
#if $param_extraction_keep_unannotated_precursor:
  -extraction:keep_unannotated_precursor
  #if " " in str($param_extraction_keep_unannotated_precursor):
    "$param_extraction_keep_unannotated_precursor"
  #else
    $param_extraction_keep_unannotated_precursor
  #end if
#end if
#if $param_extraction_min_reporter_intensity:
  -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity
#end if
#if $param_extraction_discard_low_intensity_quantifications:
  -extraction:discard_low_intensity_quantifications
#end if
#if $param_extraction_min_precursor_purity:
  -extraction:min_precursor_purity $param_extraction_min_precursor_purity
#end if
#if $param_itraq4plex_channel_114_description:
  -itraq4plex:channel_114_description     "$param_itraq4plex_channel_114_description"
#end if
#if $param_itraq4plex_channel_115_description:
  -itraq4plex:channel_115_description     "$param_itraq4plex_channel_115_description"
#end if
#if $param_itraq4plex_channel_116_description:
  -itraq4plex:channel_116_description     "$param_itraq4plex_channel_116_description"
#end if
#if $param_itraq4plex_channel_117_description:
  -itraq4plex:channel_117_description     "$param_itraq4plex_channel_117_description"
#end if
#if $param_itraq4plex_reference_channel:
  -itraq4plex:reference_channel $param_itraq4plex_reference_channel
#end if

#if $rep_param_itraq4plex_correction_matrix:
-itraq4plex:correction_matrix
  #for token in $rep_param_itraq4plex_correction_matrix:
    #if " " in str(token):
      "$token.param_itraq4plex_correction_matrix"
    #else
      $token.param_itraq4plex_correction_matrix
    #end if
  #end for
#end if
#if $param_itraq8plex_channel_113_description:
  -itraq8plex:channel_113_description     "$param_itraq8plex_channel_113_description"
#end if
#if $param_itraq8plex_channel_114_description:
  -itraq8plex:channel_114_description     "$param_itraq8plex_channel_114_description"
#end if
#if $param_itraq8plex_channel_115_description:
  -itraq8plex:channel_115_description     "$param_itraq8plex_channel_115_description"
#end if
#if $param_itraq8plex_channel_116_description:
  -itraq8plex:channel_116_description     "$param_itraq8plex_channel_116_description"
#end if
#if $param_itraq8plex_channel_117_description:
  -itraq8plex:channel_117_description     "$param_itraq8plex_channel_117_description"
#end if
#if $param_itraq8plex_channel_118_description:
  -itraq8plex:channel_118_description     "$param_itraq8plex_channel_118_description"
#end if
#if $param_itraq8plex_channel_119_description:
  -itraq8plex:channel_119_description     "$param_itraq8plex_channel_119_description"
#end if
#if $param_itraq8plex_channel_121_description:
  -itraq8plex:channel_121_description     "$param_itraq8plex_channel_121_description"
#end if
#if $param_itraq8plex_reference_channel:
  -itraq8plex:reference_channel $param_itraq8plex_reference_channel
#end if

#if $rep_param_itraq8plex_correction_matrix:
-itraq8plex:correction_matrix
  #for token in $rep_param_itraq8plex_correction_matrix:
    #if " " in str(token):
      "$token.param_itraq8plex_correction_matrix"
    #else
      $token.param_itraq8plex_correction_matrix
    #end if
  #end for
#end if
#if $param_quantification_isotope_correction:
  -quantification:isotope_correction
  #if " " in str($param_quantification_isotope_correction):
    "$param_quantification_isotope_correction"
  #else
    $param_quantification_isotope_correction
  #end if
#end if
#if $param_quantification_normalization:
  -quantification:normalization
#end if
#if $param_tmt10plex_channel_126_description:
  -tmt10plex:channel_126_description     "$param_tmt10plex_channel_126_description"
#end if
#if $param_tmt10plex_channel_127N_description:
  -tmt10plex:channel_127N_description     "$param_tmt10plex_channel_127N_description"
#end if
#if $param_tmt10plex_channel_127C_description:
  -tmt10plex:channel_127C_description     "$param_tmt10plex_channel_127C_description"
#end if
#if $param_tmt10plex_channel_128N_description:
  -tmt10plex:channel_128N_description     "$param_tmt10plex_channel_128N_description"
#end if
#if $param_tmt10plex_channel_128C_description:
  -tmt10plex:channel_128C_description     "$param_tmt10plex_channel_128C_description"
#end if
#if $param_tmt10plex_channel_129N_description:
  -tmt10plex:channel_129N_description     "$param_tmt10plex_channel_129N_description"
#end if
#if $param_tmt10plex_channel_129C_description:
  -tmt10plex:channel_129C_description     "$param_tmt10plex_channel_129C_description"
#end if
#if $param_tmt10plex_channel_130N_description:
  -tmt10plex:channel_130N_description     "$param_tmt10plex_channel_130N_description"
#end if
#if $param_tmt10plex_channel_130C_description:
  -tmt10plex:channel_130C_description     "$param_tmt10plex_channel_130C_description"
#end if
#if $param_tmt10plex_channel_131_description:
  -tmt10plex:channel_131_description     "$param_tmt10plex_channel_131_description"
#end if
#if $param_tmt10plex_reference_channel:
  -tmt10plex:reference_channel
  #if " " in str($param_tmt10plex_reference_channel):
    "$param_tmt10plex_reference_channel"
  #else
    $param_tmt10plex_reference_channel
  #end if
#end if

#if $rep_param_tmt10plex_correction_matrix:
-tmt10plex:correction_matrix
  #for token in $rep_param_tmt10plex_correction_matrix:
    #if " " in str(token):
      "$token.param_tmt10plex_correction_matrix"
    #else
      $token.param_tmt10plex_correction_matrix
    #end if
  #end for
#end if
#if $param_tmt6plex_channel_126_description:
  -tmt6plex:channel_126_description     "$param_tmt6plex_channel_126_description"
#end if
#if $param_tmt6plex_channel_127_description:
  -tmt6plex:channel_127_description     "$param_tmt6plex_channel_127_description"
#end if
#if $param_tmt6plex_channel_128_description:
  -tmt6plex:channel_128_description     "$param_tmt6plex_channel_128_description"
#end if
#if $param_tmt6plex_channel_129_description:
  -tmt6plex:channel_129_description     "$param_tmt6plex_channel_129_description"
#end if
#if $param_tmt6plex_channel_130_description:
  -tmt6plex:channel_130_description     "$param_tmt6plex_channel_130_description"
#end if
#if $param_tmt6plex_channel_131_description:
  -tmt6plex:channel_131_description     "$param_tmt6plex_channel_131_description"
#end if
#if $param_tmt6plex_reference_channel:
  -tmt6plex:reference_channel $param_tmt6plex_reference_channel
#end if

#if $rep_param_tmt6plex_correction_matrix:
-tmt6plex:correction_matrix
  #for token in $rep_param_tmt6plex_correction_matrix:
    #if " " in str(token):
      "$token.param_tmt6plex_correction_matrix"
    #else
      $token.param_tmt6plex_correction_matrix
    #end if
  #end for
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_extraction_precursor_isotope_deviation:
  -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation
#end if
    #if $adv_opts.param_extraction_purity_interpolation:
  -extraction:purity_interpolation
  #if " " in str($adv_opts.param_extraction_purity_interpolation):
    "$adv_opts.param_extraction_purity_interpolation"
  #else
    $adv_opts.param_extraction_purity_interpolation
  #end if
#end if
#end if
</command>
  <inputs>
    <param name="param_type" display="radio" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
      <option value="itraq4plex" selected="true">itraq4plex</option>
      <option value="itraq8plex">itraq8plex</option>
      <option value="tmt10plex">tmt10plex</option>
      <option value="tmt6plex">tmt6plex</option>
    </param>
    <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
    <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/mount/miniconda3/envs/openms2.2/share/OpenMS/IDPool/IDPool.txt)">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_extraction_select_activation" type="select" optional="False" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (" help="(-select_activation) e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering">
      <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" selected="true">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=""></option>
    </param>
    <param name="param_extraction_reporter_mass_shift" type="float" min="0.0001" max="0.5" optional="True" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help="(-reporter_mass_shift) "/>
    <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
    <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_extraction_min_reporter_intensity" type="float" min="0.0" optional="True" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help="(-min_reporter_intensity) "/>
    <param name="param_extraction_discard_low_intensity_quantifications" display="radio" type="boolean" truevalue="-extraction:discard_low_intensity_quantifications" falsevalue="" checked="false" optional="True" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help="(-discard_low_intensity_quantifications) "/>
    <param name="param_extraction_min_precursor_purity" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help="(-min_precursor_purity) "/>
    <param name="param_itraq4plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq4plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq4plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq4plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq4plex_reference_channel" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117)" help="(-reference_channel) "/>
    <repeat name="rep_param_itraq4plex_correction_matrix" min="0" max="1" title="param_itraq4plex_correction_matrix">
      <param name="param_itraq4plex_correction_matrix" type="text" size="30" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_itraq8plex_channel_113_description" type="text" size="30" label="Description for the content of the 113 channel" help="(-channel_113_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_channel_118_description" type="text" size="30" label="Description for the content of the 118 channel" help="(-channel_118_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_channel_119_description" type="text" size="30" label="Description for the content of the 119 channel" help="(-channel_119_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_channel_121_description" type="text" size="30" label="Description for the content of the 121 channel" help="(-channel_121_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itraq8plex_reference_channel" type="integer" min="113" max="121" optional="True" value="113" label="Number of the reference channel (113-121)" help="(-reference_channel) Please note that 120 is not valid"/>
    <repeat name="rep_param_itraq8plex_correction_matrix" min="0" max="1" title="param_itraq8plex_correction_matrix">
      <param name="param_itraq8plex_correction_matrix" type="text" size="30" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_quantification_isotope_correction" display="radio" type="select" optional="False" value="true" label="Enable isotope correction (highly recommended)" help="(-isotope_correction) Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_quantification_normalization" display="radio" type="boolean" truevalue="-quantification:normalization" falsevalue="" checked="false" optional="True" label="Enable normalization of channel intensities with respect to the reference channel" help="(-normalization) 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!"/>
    <param name="param_tmt10plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt10plex_reference_channel" type="select" optional="False" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="(-reference_channel) ">
      <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>
    </param>
    <repeat name="rep_param_tmt10plex_correction_matrix" min="0" max="1" title="param_tmt10plex_correction_matrix">
      <param name="param_tmt10plex_correction_matrix" type="text" size="30" 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" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_tmt6plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt6plex_channel_127_description" type="text" size="30" label="Description for the content of the 127 channel" help="(-channel_127_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt6plex_channel_128_description" type="text" size="30" label="Description for the content of the 128 channel" help="(-channel_128_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt6plex_channel_129_description" type="text" size="30" label="Description for the content of the 129 channel" help="(-channel_129_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt6plex_channel_130_description" type="text" size="30" label="Description for the content of the 130 channel" help="(-channel_130_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt6plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tmt6plex_reference_channel" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)" help="(-reference_channel) "/>
    <repeat name="rep_param_tmt6plex_correction_matrix" min="0" max="1" title="param_tmt6plex_correction_matrix">
      <param name="param_tmt6plex_correction_matrix" type="text" size="30" 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="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <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_extraction_precursor_isotope_deviation" type="float" min="0.0" optional="True" 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="(-precursor_isotope_deviation) "/>
      <param name="param_extraction_purity_interpolation" display="radio" type="select" optional="False" value="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="(-purity_interpolation) If set to false, only the precursor scan will be used">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="consensusxml"/>
  </outputs>
  <help>Calculates isobaric quantitative values for peptides


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html</help>
</tool>