<tool id="pepxml_to_xls" name="Convert PepXML to Tabular" version="0.1.1">
  <description></description>

  <requirements>
    <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
  </requirements>

  <command interpreter="python">
    pepxml_viewer_wrapper.py --input=${input} --export_spreadsheet $append_unmodified_peptide
  </command>

  <inputs>
    <param format="pepxml" name="input" type="data" label="PepXML Input"/>
    <param name="append_unmodified_peptide" type="boolean" truevalue="--append_unmodified_peptide" falsevalue="" label="Append Unmodified Peptide" help="Append unmodified peptide to tabular report for downstream analysis." />
  </inputs>

  <outputs>
    <data format="tabular" name="output" from_work_dir="input.pep.xls" />
  </outputs>

  <help>
  </help>
</tool>