<tool id="openms_decoy_database" version="0.1.0" name="Decoy Database Creator">
  <description>
    Create decoy protein/peptide databases from normal ones.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'DecoyDatabase' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=${in}
out=${out}
decoy_string=${decoy_string}
decoy_string_position=${decoy_string_position}
append=${append}
shuffle=${shuffle}
</configfile>
  </configfiles>
  <inputs>
    <param format="fasta" name="in" type="data" label="Input database"/>
    <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
    <param name="decoy_string_position" type="select" label="Decoy Position">
      <option value="suffix" selected="true">Suffix</option>
      <option value="prefix">Prefix</option>
    </param>
    <param type="boolean" name="append" label="Append to original database" checked="true" />
    <param type="select" name="shuffle" label="Decoy type">
      <option value="false" selected="true">Reverse</option>
      <option value="true">Shuffle</option>
    </param>
  </inputs>
  <outputs>
    <data format="fasta" name="out" />
  </outputs>
  <stdio>
    <exit_code range="1:"  level="fatal" description="Error creating decoy database." />
  </stdio>  
  <help>
**What it does**

Create decoy protein/peptide databases from normal ones.

**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>