view ProteinInference.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="ProteinInference" name="ProteinInference" version="1.12.0">
  <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

-in ${param_in}
-out ${param_out}
-min_peptides_per_protein ${param_min_peptides_per_protein}
${param_treat_charge_variants_separately}
${param_treat_modification_variants_separately}
-threads \${GALAXY_SLOTS:-24} 
</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 true" falsevalue="-treat_charge_variants_separately false" 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 true" falsevalue="-treat_modification_variants_separately false" 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)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file" 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

@REFERENCES@
</help>
</tool>