annotate id_file_converter.xml @ 0:ba86fd127f5a draft

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<tool id="openms_id_file_converter" version="0.1.0" name="ID File Converter">
  <description>
    Converts identification engine file formats.
  </description>
  <requirements>
    <requirement type="package">openms</requirement>
  </requirements>
  <command interpreter="python">
    openms_wrapper.py --executable 'IDFileConverter' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=${in}
in_type=${in.ext}
out=${out}
out_type=${output_type}
</configfile>
  </configfiles>
  <inputs>
    <param format="pepxml,protxml,idxml" name="in" type="data" label="Input Identification File"/>
    <param name="output_type" type="select" label="Output Type">
      <option value="idxml">idXML</option>
      <option value="pepxml">pepXM</option>
      <option value="mzid">mzIdentML</option>
      <option value="fasta">FASTA</option>
    </param>    
  </inputs>
  <outputs>
    <data format="idxml" name="out">
      <change_format>
        <when input="output_type" value="pepxml" format="pepxml" />
        <when input="output_type" value="mzid" format="mzid" />
        <when input="output_type" value="fasta" format="fasta" />
      </change_format>
    </data>
  </outputs>
  <help>
**What it does**

Shows basic information about the file, such as data ranges and file type.

**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>