<tool id="silac_analyzer" version="0.1.0" name="SILACAnalyzer">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py 
    --executable 'SILACAnalyzer' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=$input1
out=$out
sample!labels=[${labels}]
sample!missed_cleavages=${missed_cleavages}
sample!charge=${min_charge}:${max_charge}
sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide}
algorithm!rt_threshold=$rt_threshold
algorithm!rt_min=$rt_min
algorithm!intensity_cutoff=$intensity_cutoff
algorithm!intensity_correlation=$intensity_correlation
algorithm!model_deviation=$model_deviation
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" type="data" format="mzml" label="Input peak list" />
    <!-- TODO -->
    <param name="labels" type="select" multiple="true" label="Labels">
      <option value="Arg6" >Arg6</option>
      <option value="Arg10">Arg10</option>
      <option value="Lys4" >Lys4</option>
      <option value="Lys6" >Lys6</option>
      <option value="Lys8" >Lys8</option>
      <option value="dICPL4" >dICPL4</option>
      <option value="dICPL6" >dICPL6</option>
      <option value="dICPL10" >dICPL10</option>
      <option value="Methyl4" >Methyl4</option>
      <option value="Methyl8" >Methyl8</option>
      <option value="Methyl12" >Methyl12</option>
      <option value="Methyl16" >Methyl16</option>
      <option value="Methyl24" >Methyl24</option>
      <option value="Methyl32" >Methyl32</option>
    </param>
    <param name="missed_cleavages" type="integer" value="2" label="Allowed Missed Cleavages" />
    <expand macro="raw_feature_finder_params" />
    <!--
    <param name="rt_threshold" type="float" value="50" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." />
    <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." />
    <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." />
    <param name="intensity_correlation" type="float" value="0.9" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." />
    <param name="model_deviation" type="float" value="6" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) &lt; observed_ratio &lt; ( theoretic_ratio * model_deviation )." />
    <param name="min_charge" type="integer" value="1" label="Minimum Charge" />
    <param name="max_charge" type="integer" value="5" label="Maximum Charge" />
    <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" />
    <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" />
    -->
  </inputs>
  <outputs>
    <data format="consensusxml" name="out" />
  </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>