<tool id="myrimatch_adapter" version="0.1.0" name="MyriMatch (OpenMS)">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />  
  <expand macro="requires">
    <requirement type="package">myrimatch</requirement>
  </expand>
  <command interpreter="python">
    openms_wrapper.py 
    --executable '__SHELL__' --config $setup
    --executable 'MyriMatchAdapter' --config $config
  </command>
  <configfiles>
    <configfile name="setup">
      ln -s $input1 'input.mzML'; ln -s $database 'db.fasta'
    </configfile>
    <configfile name="config">[simple_options]
in=input.mzML
database=db.fasta
out=$out
myrimatch_executable=@WHICH(myrimatch)@
threads=4
variable_modifications=${variable_modifications or ''}
fixed_modifications=${fixed_modifications or ''}
precursor_mass_tolerance=$precursor_mass_tolerance
precursor_mass_tolerance_unit=$precursor_mass_tolerance_unit
fragment_mass_tolerance=$fragment_mass_tolerance
fragment_mass_tolerance_unit=$fragment_mass_tolerance_unit
min_precursor_charge=$min_precursor_charge
max_precursor_charge=$max_precursor_charge
MaxDynamicMods=$max_dynamic_mods
TicCutoffPercentage=$tic_cutoff_percentage
NumChargeStates=$num_charge_states
CleavageRules=$cleavage_rules
MinTerminiCleavages=$min_termini_cleavages
MaxMissedCleavages=$max_missed_cleavages
</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" />    
    <!-- TODO: precursor_mass_tolerance_avg -->
    <expand macro="fragment_mass_tolerance_param" />
    <expand macro="fragment_mass_tolerance_unit_param" />    
    <expand macro="precursor_charge_params" />
    <param name="max_dynamic_mods" label="Maximum Number of Dynamic Modifications" help="This parameter sets the maximum number of modified residues that may be in any candidate sequence." type="integer" value="2" />    
    <param name="cleavage_rules" label="Cleavage Rules" type="select">
      <option selected="true" value="Trypsin">Trypsin</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="Lys-C">Lys-C</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="Asp-N">Asp-N</option>
      <option value="PepsinA">PepsinA</option>
      <option value="CNBr">CNBr</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="NoEnzyme">NoEnzyme</option>
    </param>
    <param name="min_termini_cleavages" type="select" label="Minimum Number of Termini Cleavages" help=" By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest.">
      <option value="0">0</option>
      <option value="1">1</option>
      <option value="2" type="selected">2</option>
    </param>
    <param name="max_missed_cleavages" type="integer" value="-1" label="Maximum Number of Missed Cleavages" help="By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages. A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages." />
    <param name="tic_cutoff_percentage" label="Total Ion Current Cutoff Percentage" help="Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter." type="float" value="0.98" />
    <param name="num_charge_states" label="Number of Charge States" help="The number of charge states that MyriMatch will handle during all stages of the program." type="integer" value="3" />
  </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>