<?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: [Identification]-->
  <tool id="ProteinInference" name="ProteinInference" version="2.0.0">
    <description>Protein inference based on the number of identified peptides.</description>
    <macros>
      <token name="@EXECUTABLE@">ProteinInference</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>ProteinInference

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_min_peptides_per_protein:
  -min_peptides_per_protein $param_min_peptides_per_protein
#end if
#if $param_treat_charge_variants_separately:
  -treat_charge_variants_separately
#end if
#if $param_treat_modification_variants_separately:
  -treat_modification_variants_separately
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param help="(-min_peptides_per_protein) " label="Minimal number of peptides needed for a protein identification" min="1" name="param_min_peptides_per_protein" optional="True" type="integer" value="2"/>
      <param checked="false" falsevalue="" help="(-treat_charge_variants_separately) " label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" name="param_treat_charge_variants_separately" optional="True" truevalue="-treat_charge_variants_separately" type="boolean"/>
      <param checked="false" falsevalue="" help="(-treat_modification_variants_separately) " label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" name="param_treat_modification_variants_separately" optional="True" truevalue="-treat_modification_variants_separately" type="boolean"/>
      <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="xml" name="param_out"/>
    </outputs>
    <help>Protein inference based on the number of identified peptides.


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