<tool id="openms_peak_file_convert" version="0.1.0" name="Peak List File Converter">
  <description>
    Converts between different MS file formats.
  </description>
  <requirements>
    <requirement type="package">openms</requirement>
  </requirements>
  <command interpreter="python">
    openms_wrapper.py --executable 'FileConverter' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=${in}
in_type=${in.ext}
out=${out}
out_type=${out_format}
</configfile>
  </configfiles>
  <inputs>
    <param format="mzml,mgf,mzxml,ms2" name="in" type="data" label="Input mzML File"/>
    <param type="select" name="out_format" label="Output Type">
      <option value="mzml">mzML</option>
      <option value="mzxml">mzXML</option>
      <option value="mgf">MGF</option>
      <option value="ms2">MS2</option>
    </param>
  </inputs>
  <outputs>
    <data format="mzml" name="out">
      <change_format>
        <when input="out_format" value="mzxml" format="mzxml" />
        <when input="out_format" value="mgf" format="mgf" />
        <when input="out_format" value="ms2" format="ms2" />
      </change_format>
    </data>
  </outputs>
  <help>
**What it does**

Extracts portions of the data from an mzML.

**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>