<tool id="openms_pepxml_protxml_merger" version="0.1.0" name="Merge idXML from PepXML and ProtXML">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'IDMerger' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in="${pepxml} ${protxml}"
out=${out}
annotate_file_origin=${annotate_file_origin}
pepxml_protxml=true
</configfile>
  </configfiles>
  <inputs>
    <param format="idxml" name="pepxml" type="data" label="idXML from PepXML"/>
    <param format="idxml" name="protxml" type="data" label="idXML from ProtXML"/>
    <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." />
  </inputs>
  <outputs>
    <data format="idxml" name="out" />
  </outputs>
  <help>
**What it does**

Merge idXML files derived from a pepXML and corresponding protXML file.

**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>