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

-type ${param_type}
-in ${param_in}
-out ${param_out}
-out_stats ${param_out_stats}
-threads \${GALAXY_SLOTS:-24} 
-id_pool ${param_id_pool}
-algorithm:Extraction:select_activation ${param_select_activation}
-algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift}
-algorithm:Extraction:channel_active ${param_channel_active}
-algorithm:Quantification:channel_reference ${param_channel_reference}
#if $adv_opts.adv_opts_selector=='advanced':
    -out_mzq ${adv_opts.param_out_mzq}
    -algorithm:Quantification:isotope_correction:4plex ${adv_opts.param_4plex}
    -algorithm:Quantification:isotope_correction:8plex ${adv_opts.param_8plex}
    ${adv_opts.param_do_normalization}
    -algorithm:MetaInformation:Program ${adv_opts.param_Program}
#end if
</command>
  <inputs>
    <param name="param_type" type="select" optional="True" value="4plex" label="iTRAQ experiment type#br#" help="(-type)">
      <option value="4plex">4plex</option>
      <option value="8plex">8plex</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 (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_channel_active" type="text" size="20" value="114:liver 117:lung" label="Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format &lt;channel&gt;:&lt;name&gt;, e.g. &quot;114:myref&quot;,&quot;115:liver&quot;." help="(-channel_active)"/>
    <param name="param_channel_reference" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117 for 4plex)." help="(-channel_reference)"/>
    <expand macro="advanced_options">
      <param name="param_4plex" type="text" size="20" value="114:0/1/5.9/0.2 115:0/2/5.6/0.1 116:0/3/4.5/0.1 117:0.1/4/3.5/0.1" label="Override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'." help="(-4plex)"/>
      <param name="param_8plex" type="text" size="20" value="113:0/0/6.89/0.22 114:0/0.94/5.9/0.16 115:0/1.88/4.9/0.1 116:0/2.82/3.9/0.07 117:0.06/3.77/2.99/0 118:0.09/4.71/1.88/0 119:0.14/5.66/0.87/0 121:0.27/7.44/0.18/0" label="Override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'." help="(-8plex)"/>
      <param name="param_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization true" falsevalue="-algorithm:Quantification:do_normalization false" checked="false" optional="True" label="Normalize channels? 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="(-do_normalization)"/>
      <param name="param_Program" type="text" size="20" value="OpenMS::ITRAQAnalyzer" label="" help="(-Program)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/>
    <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
    <data name="param_out_stats" label="output statistics as tab-separated file (readable by R or Excel or ...)" format="data"/>
  </outputs>
  <help>**What it does**

Calculates iTRAQ quantitative values for peptides


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

@REFERENCES@
</help>
</tool>