<tool id="openms_idxml_to_peptides" version="0.1.0" name="Export peptide report from idXML ">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_exporter.py --type peptide --in ${in} --out ${out}
  </command>
  <inputs>
    <param format="idxml" name="in" type="data" label="Input Identification File"/>
  </inputs>
  <outputs>
    <data format="tabular" name="out">
    </data>
  </outputs>
  <help>
**What it does**

Extracts a peptide-level tabular report from an idXML file. The "Export idXML to Tabular" tool provides similar functionality and wraps the OpenMS program TextExporter. However the output of that program may be difficult to utilize in Galaxy and it fails under under certain conditions (e.g. on idXML files coming from PepNovo). This tool was designed for Galaxy and its output is easier to process with other tools in Galaxy.

**Citation**

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