view ProteinQuantifier.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="ProteinQuantifier" name="ProteinQuantifier" version="1.12.0">
  <description>Compute peptide and protein abundances</description>
  <macros>
    <token name="@EXECUTABLE@">ProteinQuantifier</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ProteinQuantifier

-in ${param_in}
-protxml ${param_protxml}
-out ${param_out}
-peptide_out ${param_peptide_out}
-mzTab_out ${param_mzTab_out}
-top ${param_top}
-average ${param_average}
${param_include_all}
${param_filter_charge}
${param_ratios}
${param_ratiosSILAC}
-threads \${GALAXY_SLOTS:-24} 
${param_normalize}
${param_fix_peptides}
-format:separator ${param_separator}
-format:quoting ${param_quoting}
-format:replacement ${param_replacement}
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML,consensusXML,idXML" optional="False" label="Input file" help="(-in)"/>
    <param name="param_protxml" type="data" format="idXML" optional="True" label="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." help="(-protxml)"/>
    <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top)"/>
    <param name="param_average" type="select" optional="True" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average)">
      <option value="median">median</option>
      <option value="mean">mean</option>
      <option value="sum">sum</option>
    </param>
    <param name="param_include_all" type="boolean" truevalue="-include_all true" falsevalue="-include_all false" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all)"/>
    <param name="param_filter_charge" type="boolean" truevalue="-filter_charge true" falsevalue="-filter_charge false" checked="false" optional="True" label="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." help="(-filter_charge)"/>
    <param name="param_ratios" type="boolean" truevalue="-ratios true" falsevalue="-ratios false" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output. Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) ..." help="(-ratios)"/>
    <param name="param_ratiosSILAC" type="boolean" truevalue="-ratiosSILAC true" falsevalue="-ratiosSILAC false" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output. Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)" help="(-ratiosSILAC)"/>
    <param name="param_normalize" type="boolean" truevalue="-consensus:normalize true" falsevalue="-consensus:normalize false" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize)"/>
    <param name="param_fix_peptides" type="boolean" truevalue="-consensus:fix_peptides true" falsevalue="-consensus:fix_peptides false" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." help="(-fix_peptides)"/>
    <param name="param_separator" type="text" size="20" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator)"/>
    <param name="param_quoting" type="select" optional="True" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting)">
      <option value="none">none</option>
      <option value="double">double</option>
      <option value="escape">escape</option>
    </param>
    <param name="param_replacement" type="text" size="20" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file for protein abundances" format="tabular"/>
    <data name="param_peptide_out" label="Output file for peptide abundances" format="tabular"/>
    <data name="param_mzTab_out" label="Export to mzTab.#br#Either 'out', 'peptide_out', or 'mzTab_out' are required. They can be used together." format="tabular"/>
  </outputs>
  <help>**What it does**

Compute peptide and protein abundances


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

@REFERENCES@
</help>
</tool>