<tool id="xtandem_adapter" version="0.1.0" name="X! Tandem (OpenMS)">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires">
    <requirement type="package">tandem</requirement>
  </expand>
  <command interpreter="python">
    openms_wrapper.py 
    --executable 'XTandemAdapter' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=$input1
out=$out
database=$database
xtandem_executable=@WHICH(tandem)@
variable_modifications=${variable_modifications or ''}
fixed_modifications=${fixed_modifications or ''}
precursor_mass_tolerance=$precursor_mass_tolerance
precursor_error_units=$precursor_mass_tolerance_unit
fragment_mass_tolerance=$fragment_mass_tolerance
fragment_error_units=$fragment_mass_tolerance_unit
min_precursor_charge=$min_precursor_charge
max_precursor_charge=$max_precursor_charge
cleavage_site=$cleavage_site
minimum_fragment_mz=$minimum_fragment_mz
max_valid_expect=$max_valid_expect
refinement=$refinement
semi_cleavage=$semi_cleavage
</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="fragment_mass_tolerance_unit_param" />
    <expand macro="precursor_charge_params" />
    <param name="cleavage_site" label="Cleavage Site" type="select">
      <option value="[R]|{P}">argc</option>
      <option value="[X]|[D]">aspn</option>
      <option value="[FMWY]|{P}">chymotrypsin</option>
      <option value="[R]|[X]">clostripain</option>
      <option value="[M]|{P}">cnbr</option>
      <option value="[AGILV]|{P}">elastase</option>
      <option value="[D]|{P}">formicacid</option>
      <option value="[DE]|{P}">gluc</option>
      <option value="[E]|{P}">gluc_bicarb</option>
      <option value="[W]|[X]">iodosobenzoate</option>
      <option value="[K]|[P]">lysc</option>
      <option value="[K]|[X]">lysc-p</option>
      <option value="[X]|[K]">lysn</option>
      <option value="[X]|[AKRS]">lysn_promisc</option>
      <option value="[X]|[X]">nonspecific</option>
      <option value="[FL]|[X]">pepsina</option>
      <option value="[P]|[X]">protein_endopeptidase</option>
      <option value="[E]|[X]">staph_protease</option>
      <option value="[KR]|{P}" selected="true">trypsin</option>
      <option value="[DEKR]|{P}">trypsin_gluc</option>
      <option value="[K]|{P}">trypsin_k</option>
      <option value="[R]|{P}">trypsin_r</option>
      <sanitizer>
        <valid>
          <add value="{"/>
          <add value="}"/>
          <add value="|"/>
          <add value="["/>
          <add value="]"/>
        </valid>
      </sanitizer>      
    </param>
    <param name="minimum_fragment_mz" label="Minimum Fragment m/z" value="150" type="float" />
    <param name="max_valid_expect" label="Maximum Valid E-Value to be Reported" value=".1" type="float" />
    <param name="semi_cleavage" type="boolean" label="Enable Semi-Cleavage" checked="false" truevalue="true" falsevalue="false" help="If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag." />
    <param name="refinement" type="boolean" label="Enable Refinement" checked="false" truevalue="true" falsevalue="false" help="Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag." />
  </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>