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annotate msgf2pin.xml @ 0:3a49065a05d6 draft

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