<tool id="compnovo" version="0.1.0" name="CompNovo (OpenMS)">
  <description>
    Performs a de novo peptide identification using the CompNovo engine.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    #if str($mode) == "cid"
    #set $executable = "CompNovoCID"
    #else
    #set $executable = "CompNovo"
    #end if
    openms_wrapper.py --executable '$executable' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=${input1}
out=${out}
#set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods])
#if $fixed_mods_str
algorithm!fixed_modifications=$fixed_mods_str
#end if
#set $variable_mods_str=",".join([str($variable_mod.fixed_mod) for $variable_mod in $variable_mods])
#if $variable_mods_str
algorithm!variable_modifications=$variable_mods_str
#end if
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" type="data" format="mzml" label="Input peak list" />
    <param name="mode" type="select" label="Mode">
      <option value="cid">CID-only</option>
      <option value="cidetd">CID/ETD</option>
    </param>
    <repeat name="fixed_mods" title="Fixed Modification">
      <param name="fixed_mod" type="select" label="Fixed Modification">
        <options from_file="openms_mods.loc">
          <column name="name" index="0" />
          <column name="value" index="0" />
        </options>
      </param>
    </repeat>
    <repeat name="variable_mods" title="Variable Modification">
      <param name="variable_mod" type="select" label="Variable Modification">
        <options from_file="openms_mods.loc">
          <column name="name" index="0"/>
          <column name="value" index="0" />
        </options>
      </param>
    </repeat>
  </inputs>
  <outputs>
    <data format="idxml" name="out" />
  </outputs>
  <help>
**What it does**

De novo peptide sequencing of mass spectrometry 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.`` and ``Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, et al.: De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis 2009, 30:3736-3747.``

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