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<?xml version='1.0' encoding='UTF-8'?>
<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="1.12.0">
  <description>Calculates isobaric quantitative values for peptides</description>
  <macros>
    <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IsobaricAnalyzer

-type ${param_type}
-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
-id_pool ${param_id_pool}
-extraction:select_activation ${param_select_activation}
-extraction:reporter_mass_shift ${param_reporter_mass_shift}
-extraction:min_precursor_intensity ${param_min_precursor_intensity}
${param_keep_unannotated_precursor}
-extraction:min_reporter_intensity ${param_min_reporter_intensity}
${param_discard_low_intensity_quantifications}
-extraction:min_precursor_purity ${param_min_precursor_purity}
-itraq4plex:channel_114_description ${param_channel_114_description}
-itraq4plex:channel_115_description ${param_channel_115_description}
-itraq4plex:channel_116_description ${param_channel_116_description}
-itraq4plex:channel_117_description ${param_channel_117_description}
-itraq4plex:reference_channel ${param_reference_channel}
-itraq4plex:correction_matrix ${param_correction_matrix}
-itraq8plex:channel_113_description ${param_channel_113_description}
-itraq8plex:channel_114_description ${param_channel_114_description}
-itraq8plex:channel_115_description ${param_channel_115_description}
-itraq8plex:channel_116_description ${param_channel_116_description}
-itraq8plex:channel_117_description ${param_channel_117_description}
-itraq8plex:channel_118_description ${param_channel_118_description}
-itraq8plex:channel_119_description ${param_channel_119_description}
-itraq8plex:channel_121_description ${param_channel_121_description}
-itraq8plex:reference_channel ${param_reference_channel}
-itraq8plex:correction_matrix ${param_correction_matrix}
${param_isotope_correction}
${param_normalization}
-tmt10plex:channel_126_description ${param_channel_126_description}
-tmt10plex:channel_127N_description ${param_channel_127N_description}
-tmt10plex:channel_127C_description ${param_channel_127C_description}
-tmt10plex:channel_128N_description ${param_channel_128N_description}
-tmt10plex:channel_128C_description ${param_channel_128C_description}
-tmt10plex:channel_129N_description ${param_channel_129N_description}
-tmt10plex:channel_129C_description ${param_channel_129C_description}
-tmt10plex:channel_130N_description ${param_channel_130N_description}
-tmt10plex:channel_130C_description ${param_channel_130C_description}
-tmt10plex:channel_131_description ${param_channel_131_description}
-tmt10plex:reference_channel ${param_reference_channel}
-tmt10plex:correction_matrix ${param_correction_matrix}
-tmt6plex:channel_126_description ${param_channel_126_description}
-tmt6plex:channel_127_description ${param_channel_127_description}
-tmt6plex:channel_128_description ${param_channel_128_description}
-tmt6plex:channel_129_description ${param_channel_129_description}
-tmt6plex:channel_130_description ${param_channel_130_description}
-tmt6plex:channel_131_description ${param_channel_131_description}
-tmt6plex:reference_channel ${param_reference_channel}
-tmt6plex:correction_matrix ${param_correction_matrix}
#if $adv_opts.adv_opts_selector=='advanced':
    -extraction:precursor_isotope_deviation ${adv_opts.param_precursor_isotope_deviation}
#end if
</command>
  <inputs>
    <param name="param_type" type="select" optional="True" value="itraq4plex" label="Isobaric Quantitation method used in the experiment." help="(-type)">
      <option value="itraq4plex">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="20" label="ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /home/thouwaar/Projects/OpenMS/share/OpenMS/IDPool/IDPool.txt)" help="(-id_pool)"/>
    <param name="param_select_activation" type="select" optional="True" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering." help="(-select_activation)">
      <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=""></option>
    </param>
    <param name="param_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position." help="(-reporter_mass_shift)"/>
    <param name="param_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation." help="(-min_precursor_intensity)"/>
    <param name="param_keep_unannotated_precursor" type="boolean" truevalue="-extraction:keep_unannotated_precursor true" falsevalue="-extraction:keep_unannotated_precursor false" checked="true" optional="True" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not." help="(-keep_unannotated_precursor)"/>
    <param name="param_min_reporter_intensity" type="float" min="0.0" optional="True" value="0.0" label="Minimum intenesity of the individual reporter ions to be used extracted." help="(-min_reporter_intensity)"/>
    <param name="param_discard_low_intensity_quantifications" type="boolean" truevalue="-extraction:discard_low_intensity_quantifications true" falsevalue="-extraction:discard_low_intensity_quantifications false" 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_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 precursor." help="(-min_precursor_purity)"/>
    <param name="param_channel_114_description" type="text" size="20" label="Description for the content of the 114 channel." help="(-channel_114_description)"/>
    <param name="param_channel_115_description" type="text" size="20" label="Description for the content of the 115 channel." help="(-channel_115_description)"/>
    <param name="param_channel_116_description" type="text" size="20" label="Description for the content of the 116 channel." help="(-channel_116_description)"/>
    <param name="param_channel_117_description" type="text" size="20" label="Description for the content of the 117 channel." help="(-channel_117_description)"/>
    <param name="param_reference_channel" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117)." help="(-reference_channel)"/>
    <param name="param_correction_matrix" type="text" size="20" 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="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
    <param name="param_channel_113_description" type="text" size="20" label="Description for the content of the 113 channel." help="(-channel_113_description)"/>
    <param name="param_channel_114_description" type="text" size="20" label="Description for the content of the 114 channel." help="(-channel_114_description)"/>
    <param name="param_channel_115_description" type="text" size="20" label="Description for the content of the 115 channel." help="(-channel_115_description)"/>
    <param name="param_channel_116_description" type="text" size="20" label="Description for the content of the 116 channel." help="(-channel_116_description)"/>
    <param name="param_channel_117_description" type="text" size="20" label="Description for the content of the 117 channel." help="(-channel_117_description)"/>
    <param name="param_channel_118_description" type="text" size="20" label="Description for the content of the 118 channel." help="(-channel_118_description)"/>
    <param name="param_channel_119_description" type="text" size="20" label="Description for the content of the 119 channel." help="(-channel_119_description)"/>
    <param name="param_channel_121_description" type="text" size="20" label="Description for the content of the 121 channel." help="(-channel_121_description)"/>
    <param name="param_reference_channel" type="integer" min="113" max="121" optional="True" value="113" label="Number of the reference channel (113-121). Please note that 120 is not valid." help="(-reference_channel)"/>
    <param name="param_correction_matrix" type="text" size="20" 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="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
    <param name="param_isotope_correction" type="boolean" truevalue="-quantification:isotope_correction true" falsevalue="-quantification:isotope_correction false" checked="true" optional="True" label="Enable isotope correction (highly recommended). Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results." help="(-isotope_correction)"/>
    <param name="param_normalization" type="boolean" truevalue="-quantification:normalization true" falsevalue="-quantification:normalization false" checked="false" optional="True" label="Enable normalization of channel intensities with respect to the reference channel. 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!" help="(-normalization)"/>
    <param name="param_channel_126_description" type="text" size="20" label="Description for the content of the 126 channel." help="(-channel_126_description)"/>
    <param name="param_channel_127N_description" type="text" size="20" label="Description for the content of the 127N channel." help="(-channel_127N_description)"/>
    <param name="param_channel_127C_description" type="text" size="20" label="Description for the content of the 127C channel." help="(-channel_127C_description)"/>
    <param name="param_channel_128N_description" type="text" size="20" label="Description for the content of the 128N channel." help="(-channel_128N_description)"/>
    <param name="param_channel_128C_description" type="text" size="20" label="Description for the content of the 128C channel." help="(-channel_128C_description)"/>
    <param name="param_channel_129N_description" type="text" size="20" label="Description for the content of the 129N channel." help="(-channel_129N_description)"/>
    <param name="param_channel_129C_description" type="text" size="20" label="Description for the content of the 129C channel." help="(-channel_129C_description)"/>
    <param name="param_channel_130N_description" type="text" size="20" label="Description for the content of the 130N channel." help="(-channel_130N_description)"/>
    <param name="param_channel_130C_description" type="text" size="20" label="Description for the content of the 130C channel." help="(-channel_130C_description)"/>
    <param name="param_channel_131_description" type="text" size="20" label="Description for the content of the 131 channel." help="(-channel_131_description)"/>
    <param name="param_reference_channel" type="select" optional="True" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)." help="(-reference_channel)">
      <option value="126">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>
    <param name="param_correction_matrix" type="text" size="20" 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="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
    <param name="param_channel_126_description" type="text" size="20" label="Description for the content of the 126 channel." help="(-channel_126_description)"/>
    <param name="param_channel_127_description" type="text" size="20" label="Description for the content of the 127 channel." help="(-channel_127_description)"/>
    <param name="param_channel_128_description" type="text" size="20" label="Description for the content of the 128 channel." help="(-channel_128_description)"/>
    <param name="param_channel_129_description" type="text" size="20" label="Description for the content of the 129 channel." help="(-channel_129_description)"/>
    <param name="param_channel_130_description" type="text" size="20" label="Description for the content of the 130 channel." help="(-channel_130_description)"/>
    <param name="param_channel_131_description" type="text" size="20" label="Description for the content of the 131 channel." help="(-channel_131_description)"/>
    <param name="param_reference_channel" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)." help="(-reference_channel)"/>
    <param name="param_correction_matrix" type="text" size="20" 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="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
    <expand macro="advanced_options">
      <param name="param_precursor_isotope_deviation" type="float" min="0.0" optional="True" value="0.02" label="Maximum allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor." help="(-precursor_isotope_deviation)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/>
  </outputs>
  <help>**What it does**

Calculates isobaric quantitative values for peptides


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

@REFERENCES@
</help>
</tool>