<tool id="omssa_adapter" version="0.1.0" name="OMSSA (OpenMS)">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires">
    <requirement type="package">omssa</requirement>
    <requirement type="package">blast+</requirement>
  </expand>
  <command interpreter="python">
    openms_wrapper.py
    --executable '__SHELL__' --config $setup
    --executable 'OMSSAAdapter' --config $config
  </command>
  <configfiles>
    <configfile name="setup">
      ln -s $database db.fasta; makeblastdb -dbtype prot -parse_seqids -in 'db.fasta'
    </configfile>
    <configfile name="config">[simple_options]
in=$input1
out=$out
database=db.fasta.psq
omssa_executable=@WHICH(omssacl)@
variable_modifications=${variable_modifications or ''}
fixed_modifications=${fixed_modifications or ''}
precursor_mass_tolerance=$precursor_mass_tolerance
#if $precursor_mass_tolerance_unit == "ppm"
precursor_mass_tolerance_unit_ppm=true
#end if
fragment_mass_tolerance=$fragment_mass_tolerance
min_precursor_charge=$min_precursor_charge
max_precursor_charge=$max_precursor_charge
v=$v
e=$e
hl=$hl
he=$he
threads=4
</configfile>
  </configfiles>
  <inputs>
    <expand macro="id_inputs" />
    <expand macro="fixed_modifications_param" />
    <expand macro="variable_modifications_param" />
    <expand macro="precursor_mass_tolerance_param" />
    <expand macro="precursor_mass_tolerance_unit_param" />
    <expand macro="fragment_mass_tolerance_param" />
    <expand macro="precursor_charge_params" />
    <param name="v" label="Maximum Number of Missed Cleavages" value="1" type="integer" />
    <param name="e" label="Enzyme" type="select">
      <option value="0" selected="true">Trypsin</option>
      <option value="1">Arg-C</option>
      <option value="2">CNBr</option>
      <option value="3">Chymotrypsin (FYWL)</option>
      <option value="4">Formic Acid</option>
      <option value="5">Lys-C</option>
      <option value="6">Lys-C, no P rule</option>
      <option value="7">Pepsin A</option>
      <option value="8">Trypsin+CNBr</option>
      <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
      <option value="10">Trypsin, no P rule</option>
      <option value="11">Whole protein</option>
      <option value="12">Asp-N</option>
      <option value="13">Glu-C</option>
      <option value="14">Asp-N+Glu-C</option>
      <option value="15">Top-Down</option>
      <option value="16">Semi-Tryptic</option>
      <option value="17">No Enzyme</option>
      <option value="18">Chymotrypsin, no P rule (FYWL)</option>
      <option value="19">Asp-N (DE)</option>
      <option value="20">Glu-C (DE)</option>
      <option value="21">Lys-N (K)</option>
      <option value="22">Thermolysin, no P rule</option>
      <option value="23">Semi-Chymotrypsin (FYWL)</option>
      <option value="24">Semi-Glu-C</option>
    </param>
    <param name="hl" label="Maximum Hits Per Spectrum" type="integer" value="30" />
    <param name="he" label="Maximum Hits Per Spectrum" type="float" value="1000" help="The maximum e-value allowed in the hit list. If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported. " />    
  </inputs>
  <expand macro="id_outputs" />
  <help>
**What it does**


**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 ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.

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