<tool id="openms_id_merger" version="0.1.0" name="ID Merger">
  <description>
    Merges several idXML files into one idXML file.
  </description>
  <requirements>
    <requirement type="package">openms</requirement>
  </requirements>
  <command interpreter="python">
    openms_wrapper.py --executable 'IDMerger' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
#set $in_str = ""      
#for $input in $inputs
#set $in_str = $input.input + " " $in_str
#end for
in="${in_str}"
out=${out}
annotate_file_origin=${annotate_file_origin}
</configfile>
  </configfiles>
  <inputs>
    <repeat name="inputs">
      <param format="idxml" name="input" type="data" label="idXML Input"/>
    </repeat>
    <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**

The peptide hits and protein hits of the input files will be written into the single output file. In general, the number of idXML files that can be merged into one file is not limited.

The combination of search engine and processing date/time should be unique for every identification run over all input files. If this is not the case, the date/time of a conflicting run will be increased in steps of seconds until the combination is unique.

**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>