<?xml version='1.0' encoding='UTF-8'?>
<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="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 name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_min_peptides_per_protein" type="integer" min="1" optional="True" value="2" label="Minimal number of peptides needed for a protein identification" help="(-min_peptides_per_protein) "/>
    <param name="param_treat_charge_variants_separately" type="boolean" truevalue="-treat_charge_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" help="(-treat_charge_variants_separately) "/>
    <param name="param_treat_modification_variants_separately" type="boolean" truevalue="-treat_modification_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" help="(-treat_modification_variants_separately) "/>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
  </outputs>
  <help>**What it does**

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>
  <expand macro="references"/>
</tool>