<tool id="openms_id_filter" version="0.1.0" name="ID Filter">
  <description>
    Filters protein identification engine results by different criteria.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'IDFilter' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=$input1
out=$output
score!pep=$peptide_score
score!prot=$protein_score
thresh!pep=$peptide_threshold
thresh!prot=$protein_threshold
best!n_peptide_hits=$n_peptide_hits
best!n_protein_hits=$n_protein_hits
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" label="Input" type="data" format="idxml" />
    <param name="n_peptide_hits" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0). " value="0" type="integer" />
    <param name="n_protein_hits" label="Keep only the 'n' highest scoring protein hits per spectrum (for n>0). " value="0" type="integer" />
    <param name="peptide_score" label="Peptide Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" />
    <param name="protein_score" label="Protein Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" />
    <param name="peptide_threshold" label="Peptide Threshold" help="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" />
    <param name="protein_threshold" label="Protein Threshold" help="Keep a protein hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" />
  </inputs>
  <outputs>
    <data format="idxml" name="output" />
  </outputs>
  <help>
**What it does**

This tool is used to filter the identifications found by a peptide/protein identification tool like Mascot. Different filters can be applied.

**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>