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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="1.12.0">
  <description>Determination of peak ratios in LC-MS data</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderMultiplex

-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:labels ${param_labels}
-algorithm:charge ${param_charge}
-algorithm:rt_typical ${param_rt_typical}
-algorithm:rt_min ${param_rt_min}
-algorithm:mz_tolerance ${param_mz_tolerance}
-algorithm:mz_unit ${param_mz_unit}
-algorithm:intensity_cutoff ${param_intensity_cutoff}
-algorithm:peptide_similarity ${param_peptide_similarity}
-algorithm:averagine_similarity ${param_averagine_similarity}
-algorithm:missed_cleavages ${param_missed_cleavages}
#if $adv_opts.adv_opts_selector=='advanced':
    -out_features ${adv_opts.param_out_features}
    -out_mzq ${adv_opts.param_out_mzq}
    -out_debug ${adv_opts.param_out_debug}
    -algorithm:isotopes_per_peptide ${adv_opts.param_isotopes_per_peptide}
    ${adv_opts.param_knock_out}
    -labels:Arg6 ${adv_opts.param_Arg6}
    -labels:Arg10 ${adv_opts.param_Arg10}
    -labels:Lys4 ${adv_opts.param_Lys4}
    -labels:Lys6 ${adv_opts.param_Lys6}
    -labels:Lys8 ${adv_opts.param_Lys8}
    -labels:Dimethyl0 ${adv_opts.param_Dimethyl0}
    -labels:Dimethyl4 ${adv_opts.param_Dimethyl4}
    -labels:Dimethyl6 ${adv_opts.param_Dimethyl6}
    -labels:Dimethyl8 ${adv_opts.param_Dimethyl8}
    -labels:ICPL0 ${adv_opts.param_ICPL0}
    -labels:ICPL4 ${adv_opts.param_ICPL4}
    -labels:ICPL6 ${adv_opts.param_ICPL6}
    -labels:ICPL10 ${adv_opts.param_ICPL10}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)" help="(-in)"/>
    <param name="param_labels" type="text" size="20" value="[][Lys8,Arg10]" label="Labels used for labelling the samples. [...] specifies the labels for a single sample. For example#br##br#[][Lys8,Arg10]        ... SILAC#br#[][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC#br#[Dimethyl0][Dimethyl6]        ... Dimethyl#br#[Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl#br#[ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL" help="(-labels)"/>
    <param name="param_charge" type="text" size="20" value="1:4" label="Range of charge states in the sample, i.e. min charge : max charge." help="(-charge)"/>
    <param name="param_rt_typical" type="float" min="0.0" optional="True" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)" help="(-rt_typical)"/>
    <param name="param_rt_min" type="float" min="0.0" optional="True" value="2.0" label="Lower bound for the retention time [s]. (Any peptides seen for a shorter time period are not reported.)" help="(-rt_min)"/>
    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="6.0" label="m/z tolerance for search of peak patterns." help="(-mz_tolerance)"/>
    <param name="param_mz_unit" type="select" optional="True" value="ppm" label="Unit of the 'mz_tolerance' parameter." help="(-mz_unit)">
      <option value="Da">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <param name="param_intensity_cutoff" type="float" min="0.0" optional="True" value="1000.0" label="Lower bound for the intensity of isotopic peaks." help="(-intensity_cutoff)"/>
    <param name="param_peptide_similarity" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern. This parameter is a lower bound on their similarity." help="(-peptide_similarity)"/>
    <param name="param_averagine_similarity" type="float" min="0.0" max="1.0" optional="True" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position. This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model." help="(-averagine_similarity)"/>
    <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion." help="(-missed_cleavages)"/>
    <expand macro="advanced_options">
      <param name="param_out_debug" type="text" size="20" label="Directory for debug output." help="(-out_debug)"/>
      <param name="param_isotopes_per_peptide" type="text" size="20" value="3:6" label="Range of isotopes per peptide in the sample. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " help="(-isotopes_per_peptide)"/>
      <param name="param_knock_out" type="boolean" truevalue="-algorithm:knock_out true" falsevalue="-algorithm:knock_out false" checked="true" optional="True" label="Is it likely that knock-outs are present? (Supported for doublex, triplex and quadruplex experiments only.)" help="(-knock_out)"/>
      <param name="param_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Arg6)"/>
      <param name="param_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help="(-Arg10)"/>
      <param name="param_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help="(-Lys4)"/>
      <param name="param_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Lys6)"/>
      <param name="param_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help="(-Lys8)"/>
      <param name="param_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help="(-Dimethyl0)"/>
      <param name="param_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help="(-Dimethyl4)"/>
      <param name="param_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help="(-Dimethyl6)"/>
      <param name="param_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help="(-Dimethyl8)"/>
      <param name="param_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help="(-ICPL0)"/>
      <param name="param_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help="(-ICPL4)"/>
      <param name="param_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help="(-ICPL6)"/>
      <param name="param_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help="(-ICPL10)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group." format="consensusXML"/>
    <data name="param_out_features" label="Optional output file containing the individual peptide features in 'out'." format="featureXML"/>
    <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
  </outputs>
  <help>**What it does**

Determination of peak ratios in LC-MS data


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

@REFERENCES@
</help>
</tool>