view TMTAnalyzer.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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="TMTAnalyzer" name="TMTAnalyzer" version="2.0.0">
    <description>Calculates TMT quantitative values for peptides</description>
    <macros>
      <token name="@EXECUTABLE@">TMTAnalyzer</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>TMTAnalyzer

#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
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_Extraction_select_activation:
  -algorithm:Extraction:select_activation
  #if &quot; &quot; in str($param_algorithm_Extraction_select_activation):
    &quot;$param_algorithm_Extraction_select_activation&quot;
  #else
    $param_algorithm_Extraction_select_activation
  #end if
#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 $rep_param_algorithm_Extraction_channel_active:
    #if &quot; &quot; in str(token):
      &quot;$token.param_algorithm_Extraction_channel_active&quot;
    #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_tmt_6plex:
-algorithm:Quantification:isotope_correction:tmt-6plex
  #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
    #if &quot; &quot; in str(token):
      &quot;$token.param_algorithm_Quantification_isotope_correction_tmt_6plex&quot;
    #else
      $token.param_algorithm_Quantification_isotope_correction_tmt_6plex
    #end if
  #end for
#end if
    #if $adv_opts.param_algorithm_Quantification_do_normalization:
  -algorithm:Quantification:do_normalization
#end if
    #if $adv_opts.param_algorithm_MetaInformation_Program:
  -algorithm:MetaInformation:Program     &quot;$adv_opts.param_algorithm_MetaInformation_Program&quot;
#end if
#end if
</command>
    <inputs>
      <param format="mzml" help="(-in) " label="input raw/picked data file" name="param_in" optional="False" type="data"/>
      <param help="(-select_activation) Set to empty string if you want to disable filtering" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ)" name="param_algorithm_Extraction_select_activation" optional="True" type="select" value="High-energy collision-induced dissociation">
        <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 help="(-reporter_mass_shift) " label="Allowed shift (left to right) in Da from the expected position" max="0.5" min="1e-08" name="param_algorithm_Extraction_reporter_mass_shift" optional="True" type="float" value="0.1"/>
      <repeat max="1" min="0" name="rep_param_algorithm_Extraction_channel_active" title="param_algorithm_Extraction_channel_active">
        <param help="(-channel_active) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format &lt;channel&gt;:&lt;name&gt;," name="param_algorithm_Extraction_channel_active" size="30" type="text" value="126:liver 131:lung">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param help="(-channel_reference) " label="Number of the reference channel (126-131)" max="131" min="126" name="param_algorithm_Quantification_channel_reference" optional="True" type="integer" value="126"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <repeat max="1" min="0" name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" title="param_algorithm_Quantification_isotope_correction_tmt_6plex">
          <param help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'" 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; ;" name="param_algorithm_Quantification_isotope_correction_tmt_6plex" size="30" type="text" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0">
            <sanitizer>
              <valid initial="string.printable">
                <remove value="'"/>
                <remove value="&quot;"/>
              </valid>
            </sanitizer>
          </param>
        </repeat>
        <param checked="false" falsevalue="" 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!" label="Normalize channels?" name="param_algorithm_Quantification_do_normalization" optional="True" truevalue="-algorithm:Quantification:do_normalization" type="boolean"/>
        <param help="(-Program) " label="" name="param_algorithm_MetaInformation_Program" size="30" type="text" value="OpenMS::TMTAnalyzer">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </expand>
    </inputs>
    <outputs>
      <data format="consensusxml" name="param_out"/>
      <data format="mzq" name="param_out_mzq"/>
      <data format="tabular" name="param_out_stats"/>
    </outputs>
    <help>Calculates TMT quantitative values for peptides


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