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<tool id="openms_feature_finder_raw" version="0.1.0" name="Feature Finder (Raw)">
  <description>
    Identifies peptide features in raw (i.e. profile) LC-MS data.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'FeatureFinderRaw' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=$input1
out=$output
sample!charge=${min_charge}:${max_charge}
sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide}
algorithm!rt_threshold=$rt_threshold
algorithm!rt_min=$rt_min
algorithm!intensity_cutoff=$intensity_cutoff
algorithm!intensity_correlation=$intensity_correlation
algorithm!model_deviation=$model_deviation
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="mzML Input" type="data" format="mzml" />
    <expand macro="raw_feature_finder_params" />
  </inputs>
  <outputs>
    <data format="featurexml" name="output" />
  </outputs>
  <help>
**What it does**

FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data.

**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>