annotate ITRAQAnalyzer.xml @ 0:014f4e11a3d9 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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="ITRAQAnalyzer" name="ITRAQAnalyzer" version="2.1.0">
  <description>Calculates iTRAQ quantitative values for peptides</description>
  <macros>
    <token name="@EXECUTABLE@">ITRAQAnalyzer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ITRAQAnalyzer

#if $param_type:
  -type $param_type
#end if
#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_mzq:
  -out_mzq $param_out_mzq
#end if
#if $param_out_stats:
  -out_stats $param_out_stats
#end if
#if $param_id_pool:
  -id_pool     "$param_id_pool"
#end if
#if $param_algorithm_Extraction_select_activation:
  -algorithm:Extraction:select_activation $param_algorithm_Extraction_select_activation
#end if
#if $param_algorithm_Extraction_reporter_mass_shift:
  -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift
#end if

#if $rep_param_algorithm_Extraction_channel_active:
-algorithm:Extraction:channel_active
  #for token in $rep_param_algorithm_Extraction_channel_active:
    #if " " in str(token):
      "$token.param_algorithm_Extraction_channel_active"
    #else
      $token.param_algorithm_Extraction_channel_active
    #end if
  #end for
#end if
#if $param_algorithm_Quantification_channel_reference:
  -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    
#if $rep_param_algorithm_Quantification_isotope_correction_4plex:
-algorithm:Quantification:isotope_correction:4plex
  #for token in $rep_param_algorithm_Quantification_isotope_correction_4plex:
    #if " " in str(token):
      "$token.param_algorithm_Quantification_isotope_correction_4plex"
    #else
      $token.param_algorithm_Quantification_isotope_correction_4plex
    #end if
  #end for
#end if
    
#if $rep_param_algorithm_Quantification_isotope_correction_8plex:
-algorithm:Quantification:isotope_correction:8plex
  #for token in $rep_param_algorithm_Quantification_isotope_correction_8plex:
    #if " " in str(token):
      "$token.param_algorithm_Quantification_isotope_correction_8plex"
    #else
      $token.param_algorithm_Quantification_isotope_correction_8plex
    #end if
  #end for
#end if
    #if $adv_opts.param_algorithm_Quantification_do_normalization:
  -algorithm:Quantification:do_normalization
#end if
    #if $adv_opts.param_algorithm_MetaInformation_Program:
  -algorithm:MetaInformation:Program     "$adv_opts.param_algorithm_MetaInformation_Program"
#end if
#end if
</command>
  <inputs>
    <param name="param_type" display="radio" type="select" optional="False" value="4plex" label="iTRAQ experiment type" help="(-type) ">
      <option value="4plex" selected="true">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="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/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_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 (usually HCD for iTRAQ)" help="(-select_activation) 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_algorithm_Extraction_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) "/>
    <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active">
      <param name="param_algorithm_Extraction_channel_active" type="text" size="30" 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;," help="(-channel_active) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_algorithm_Quantification_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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <repeat name="rep_param_algorithm_Quantification_isotope_correction_4plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_4plex">
        <param name="param_algorithm_Quantification_isotope_correction_4plex" type="text" size="30" 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; ;" help="(-4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <repeat name="rep_param_algorithm_Quantification_isotope_correction_8plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_8plex">
        <param name="param_algorithm_Quantification_isotope_correction_8plex" type="text" size="30" 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; ;" help="(-8plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param name="param_algorithm_Quantification_do_normalization" display="radio" type="boolean" truevalue="-algorithm:Quantification:do_normalization" falsevalue="" checked="false" optional="True" label="Normalize channels?" help="(-do_normalization) 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_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::ITRAQAnalyzer" label="" help="(-Program) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="consensusxml"/>
    <data name="param_out_mzq" format="mzq"/>
    <data name="param_out_stats" format="tabular"/>
  </outputs>
  <help>Calculates iTRAQ quantitative values for peptides


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