<?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="ProteinQuantifier" name="ProteinQuantifier" version="2.0.0">
    <description>Compute peptide and protein abundances</description>
    <macros>
      <token name="@EXECUTABLE@">ProteinQuantifier</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>ProteinQuantifier

#if $param_in:
  -in $param_in
#end if
#if $param_protein_groups:
  -protein_groups $param_protein_groups
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_peptide_out:
  -peptide_out $param_peptide_out
#end if
#if $param_top:
  -top $param_top
#end if
#if $param_average:
  -average
  #if &quot; &quot; in str($param_average):
    &quot;$param_average&quot;
  #else
    $param_average
  #end if
#end if
#if $param_include_all:
  -include_all
#end if
#if $param_filter_charge:
  -filter_charge
#end if
#if $param_ratios:
  -ratios
#end if
#if $param_ratiosSILAC:
  -ratiosSILAC
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_consensus_normalize:
  -consensus:normalize
#end if
#if $param_consensus_fix_peptides:
  -consensus:fix_peptides
#end if
#if $param_format_separator:
  -format:separator     &quot;$param_format_separator&quot;
#end if
#if $param_format_quoting:
  -format:quoting
  #if &quot; &quot; in str($param_format_quoting):
    &quot;$param_format_quoting&quot;
  #else
    $param_format_quoting
  #end if
#end if
#if $param_format_replacement:
  -format:replacement     &quot;$param_format_replacement&quot;
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml,consensusxml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
      <param format="xml" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). &lt;br&gt;Information about indistinguishable proteins will be used for protein quantification" label="Protein inference results for the identification runs that were used to annotate the input (" name="param_protein_groups" optional="True" type="data"/>
      <param help="(-top) " label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" min="0" name="param_top" optional="True" type="integer" value="3"/>
      <param help="(-average) " label="Averaging method used to compute protein abundances from peptide abundances" name="param_average" optional="True" type="select" value="median">
        <option value="median">median</option>
        <option value="mean">mean</option>
        <option value="weighted_mean">weighted_mean</option>
        <option value="sum">sum</option>
      </param>
      <param checked="false" falsevalue="" help="(-include_all) " label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" name="param_include_all" optional="True" truevalue="-include_all" type="boolean"/>
      <param checked="false" falsevalue="" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; &lt;br&gt;for proteins, abundances will be computed based only on the most prevalent charge of each peptide. &lt;br&gt;By default, abundances are summed over all charge states" label="Distinguish between charge states of a peptide" name="param_filter_charge" optional="True" truevalue="-filter_charge" type="boolean"/>
      <param checked="false" falsevalue="" help="(-ratios) 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) " label="Add the log2 ratios of the abundance values to the output" name="param_ratios" optional="True" truevalue="-ratios" type="boolean"/>
      <param checked="false" falsevalue="" help="(-ratiosSILAC) 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)" label="Add the log2 ratios for a triple SILAC experiment to the output" name="param_ratiosSILAC" optional="True" truevalue="-ratiosSILAC" type="boolean"/>
      <param checked="false" falsevalue="" help="(-normalize) " label="Scale peptide abundances so that medians of all samples are equal" name="param_consensus_normalize" optional="True" truevalue="-consensus:normalize" type="boolean"/>
      <param checked="false" falsevalue="" help="(-fix_peptides) &lt;br&gt;With 'top 0', all peptides that occur in every sample are considered. &lt;br&gt;Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, &lt;br&gt;breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)" label="Use the same peptides for protein quantification across all samples" name="param_consensus_fix_peptides" optional="True" truevalue="-consensus:fix_peptides" type="boolean"/>
      <param help="(-separator) " label="Character(s) used to separate fields; by default, the 'tab' character is used" name="param_format_separator" size="30" type="text">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-quoting) " label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" name="param_format_quoting" optional="True" type="select" value="double">
        <option value="none">none</option>
        <option value="double">double</option>
        <option value="escape">escape</option>
      </param>
      <param help="(-replacement) " label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" name="param_format_replacement" size="30" type="text" value="_">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="tabular" name="param_out"/>
      <data format="tabular" name="param_peptide_out"/>
    </outputs>
    <help>Compute peptide and protein abundances


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