<tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0">
    <description>to create Percolator input files</description>
    <requirements>
        <requirement type="package" version="3.0">percolator</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"/>
    </stdio>
    <command>
             msgf2pin -o $pinout -e $enzyme
             #if $matches
             -m $matches
             #end if
             $aafreq $ptm $pngase $isotope
             "$target" "$decoy"
    </command>
    <inputs>
        <param name="target" type="data" format="mzid,meta2pin" label="Target MSGF+ results or metafile pointing to them" />
        <param name="decoy" type="data" format="mzid,meta2pin" label="Decoy MSGF+ results or metafile pointing to them" />
        <param name="enzyme" type="select" label="Enzyme used">
          <option value="trypsin">trypsin</option>
          <option value="no_enzyme">no enzyme</option>
          <option value="elastase">elastase</option>
          <option value="pepsin">pepsin</option>
          <option value="proteinasek">proteinase K</option>
          <option value="thermolysin">thermolysin</option>
          <option value="chymotrypsin">chymotrypsin</option>
          <option value="lys-n">lys-N</option>
          <option value="lys-c">lys-C</option>
          <option value="arg-c">arg-C</option>
          <option value="asp-n">asp-N</option>
          <option value="glu-c">glu-C</option>
        </param>
        <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" />
	<param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" />
        <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" />
        <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" />
        <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" />
    </inputs>
    <outputs>
        <data format="percin" name="pinout"/>
    </outputs>
    <tests>
        <test>
          <param name="target" value="target.mzid"/>
          <param name="decoy" value="decoy.mzid"/>
          <param name="ptm" value="true"/>
          <param name="matches" value="1"/>
          <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" />
        </test>
    </tests>
    <help>
The percolator converter msgf2pin converts mzIdentML to input for percolator.
Target and decoy inputs are MzIdentML-files of MS-GF+ from
separate target and decoy searches. Internal MS-GF+ target/decoy
analysis should be turned off, and the addFeatures options turned on.
Multiple MzIdentML-files can be merged by replacing target and decoy
filepaths with meta files. Meta files are text files containing the
the paths of mzid-files, one path per line. For successful results,
the different runs should be generated under similar conditions.
    </help>
    <citations>
        <citation type="doi">10.1021/pr400937n</citation>
    </citations>
</tool>