<tool id="openms_idxml_to_tabular" version="0.1.0" name="Export idXML to Tabular">
  <description>
    Converts identification engine file formats.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'TextExporter' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=${in}
out=${out}
$dump_type
id!first_dim_rt=$extra_rt
</configfile>
  </configfiles>
  <inputs>
    <param format="idxml" name="in" type="data" label="Input Identification File"/>
    <param name="dump_type" type="select" label="Export type">
      <option value="">Run, peptide, and protein information</option>
      <option value="id!proteins_only=true">Run and protein information only</option>
      <option value="id!peptides_only=true">Peptide information only</option>
    </param>
    <param name="extra_rt" type="boolean" label="Include RT information (if present)" />
  </inputs>
  <outputs>
    <data format="tabular" name="out">
    </data>
  </outputs>
  <help>
**What it does**

Converts idXML files to tabular.

**Citation**

For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
  </help>
</tool>