Mercurial > repos > galaxyp > percolator
comparison msgf2pin.xml @ 0:3a49065a05d6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
| author | galaxyp |
|---|---|
| date | Wed, 07 Dec 2016 16:43:51 -0500 |
| parents | |
| children | 86770eea5b09 |
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| -1:000000000000 | 0:3a49065a05d6 |
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| 1 <tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0"> | |
| 2 <description>to create Percolator input files</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.0">percolator</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:"/> | |
| 8 </stdio> | |
| 9 <command> | |
| 10 msgf2pin -o $pinout -e $enzyme | |
| 11 #if $matches | |
| 12 -m $matches | |
| 13 #end if | |
| 14 $aafreq $ptm $pngase $isotope | |
| 15 "$target" "$decoy" | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="target" type="data" format="mzid,meta2pin" label="Target MSGF+ results or metafile pointing to them" /> | |
| 19 <param name="decoy" type="data" format="mzid,meta2pin" label="Decoy MSGF+ results or metafile pointing to them" /> | |
| 20 <param name="enzyme" type="select" label="Enzyme used"> | |
| 21 <option value="trypsin">trypsin</option> | |
| 22 <option value="no_enzyme">no enzyme</option> | |
| 23 <option value="elastase">elastase</option> | |
| 24 <option value="pepsin">pepsin</option> | |
| 25 <option value="proteinasek">proteinase K</option> | |
| 26 <option value="thermolysin">thermolysin</option> | |
| 27 <option value="chymotrypsin">chymotrypsin</option> | |
| 28 <option value="lys-n">lys-N</option> | |
| 29 <option value="lys-c">lys-C</option> | |
| 30 <option value="arg-c">arg-C</option> | |
| 31 <option value="asp-n">asp-N</option> | |
| 32 <option value="glu-c">glu-C</option> | |
| 33 </param> | |
| 34 <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" /> | |
| 35 <param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" /> | |
| 36 <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" /> | |
| 37 <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" /> | |
| 38 <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" /> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data format="percin" name="pinout"/> | |
| 42 </outputs> | |
| 43 <tests> | |
| 44 <test> | |
| 45 <param name="target" value="target.mzid"/> | |
| 46 <param name="decoy" value="decoy.mzid"/> | |
| 47 <param name="ptm" value="true"/> | |
| 48 <param name="matches" value="1"/> | |
| 49 <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" /> | |
| 50 </test> | |
| 51 </tests> | |
| 52 <help> | |
| 53 The percolator converter msgf2pin converts mzIdentML to input for percolator. | |
| 54 Target and decoy inputs are MzIdentML-files of MS-GF+ from | |
| 55 separate target and decoy searches. Internal MS-GF+ target/decoy | |
| 56 analysis should be turned off, and the addFeatures options turned on. | |
| 57 Multiple MzIdentML-files can be merged by replacing target and decoy | |
| 58 filepaths with meta files. Meta files are text files containing the | |
| 59 the paths of mzid-files, one path per line. For successful results, | |
| 60 the different runs should be generated under similar conditions. | |
| 61 </help> | |
| 62 <citations> | |
| 63 <citation type="doi">10.1021/pr400937n</citation> | |
| 64 </citations> | |
| 65 </tool> |