<?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="ProteinResolver" name="ProteinResolver" version="2.0.0">
    <description>protein inference</description>
    <macros>
      <token name="@EXECUTABLE@">ProteinResolver</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>ProteinResolver

#if $param_fasta:
  -fasta $param_fasta
#end if
-in
  #for token in $param_in:
    $token
  #end for
#if $param_in_path:
  -in_path     &quot;$param_in_path&quot;
#end if
#if $param_design:
  -design $param_design
#end if
#if $param_protein_groups:
  -protein_groups $param_protein_groups
#end if
#if $param_peptide_table:
  -peptide_table $param_peptide_table
#end if
#if $param_protein_table:
  -protein_table $param_protein_table
#end if
#if $param_additional_info:
  -additional_info $param_additional_info
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_resolver_missed_cleavages:
  -resolver:missed_cleavages $param_resolver_missed_cleavages
#end if
#if $param_resolver_min_length:
  -resolver:min_length $param_resolver_min_length
#end if
#if $param_resolver_enzyme:
  -resolver:enzyme     &quot;$param_resolver_enzyme&quot;
#end if
#if $param_designer_experiment:
  -designer:experiment     &quot;$param_designer_experiment&quot;
#end if
#if $param_designer_file:
  -designer:file     &quot;$param_designer_file&quot;
#end if
#if $param_designer_separator:
  -designer:separator
  #if &quot; &quot; in str($param_designer_separator):
    &quot;$param_designer_separator&quot;
  #else
    $param_designer_separator
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="fasta" help="(-fasta) " label="Input database file" name="param_fasta" optional="False" type="data"/>
      <param format="xml,consensusxml" help="(-in) " label="Input file(s) holding experimental data" multiple="true" name="param_in" optional="True" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-in_path) Ignored if 'in' is given" label="Path to idXMLs or consensusXMLs files" name="param_in_path" size="30" type="text">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param format="txt" help="(-design) See documentation for specific format requirements" label="Text file containing the experimental design" name="param_design" optional="True" type="data"/>
      <param help="(-missed_cleavages) " label="Number of allowed missed cleavages" min="0" name="param_resolver_missed_cleavages" optional="True" type="integer" value="2"/>
      <param help="(-min_length) " label="Minimum length of peptide" min="1" name="param_resolver_min_length" optional="True" type="integer" value="6"/>
      <param help="(-enzyme) " label="Digestion enzyme" name="param_resolver_enzyme" size="30" type="text" value="Trypsin">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-experiment) " label="Identifier for the experimental design" name="param_designer_experiment" size="30" type="text" value="ExperimentalSetting">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-file) " label="Identifier for the file name" name="param_designer_file" size="30" type="text" value="File">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-separator) " label="Separator, which should be used to split a row into columns" name="param_designer_separator" optional="True" type="select" value="tab">
        <option value="tab">tab</option>
        <option value="semi-colon">semi-colon</option>
        <option value="comma">comma</option>
        <option value="whitespace">whitespace</option>
      </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_protein_groups"/>
      <data format="tabular" name="param_peptide_table"/>
      <data format="tabular" name="param_protein_table"/>
      <data format="tabular" name="param_additional_info"/>
    </outputs>
    <help>protein inference


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