Mercurial > repos > jfb > kinamine7_7
comparison KinaMine-Galaxy-7-7/Kinamine.xml @ 0:67635b462045 draft
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| author | jfb |
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| date | Tue, 20 Feb 2018 14:31:15 -0500 |
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| -1:000000000000 | 0:67635b462045 |
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| 1 <tool id="kinamine_java" name="Kinamine_7_to_7" version="0.5.0"> | |
| 2 <description>Extracts phosphorylated motifs</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="8.0.1440.1">Java</requirement> | |
| 5 </requirements> | |
| 6 <command><![CDATA[ | |
| 7 mkdir -p output && | |
| 8 java -Djava.awt.headless=true -jar '$__tool_directory__/Kinamine 7 to 7.jar' $FDRreport $reference $fdr output | |
| 9 ]]></command> | |
| 10 <inputs> | |
| 11 <param format="txt" name="FDRreport" type="data" label="Distinct Peptide Report"/> | |
| 12 <param format="fasta" name="reference" type="data" label="FASTA reference"/> | |
| 13 <param name="fdr" type="integer" value"1" min="1" max="100" label="FDR"/> | |
| 14 <param name="outGroup" type="text" value"kinase" label="Group Name"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="csv" name="Substrates" from_work_dir="output/" label="${outGroup}_Substrates.csv"/> | |
| 18 <data format="csv" name="SBF" from_work_dir="output2.csv" label="Substrate Background Frequency"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="substrates" ftype="csv" value="substrates.csv"/> | |
| 23 <param name="negatives" ftype="csv" value="negatives.csv"/> | |
| 24 <param name="SBF" ftype="csv" value="SBF.csv"/> | |
| 25 <output name="SDtable" file="SDtable.csv"/> | |
| 26 <output name="EPM" file="EPM.csv"/> | |
| 27 <output name="Characterization" file="Characterization.csv"/> | |
| 28 </test> | |
| 29 </tests> | |
| 30 | |
| 31 | |
| 32 <help><![CDATA[ | |
| 33 This takes a Distinct Peptide Report and extracts from it all phospho-motifs that were discovered at a threshold above a given FDR value. This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook. | |
| 34 | |
| 35 =========== | |
| 36 Inputs | |
| 37 =========== | |
| 38 **Distinct Peptide Report** | |
| 39 This is... ask Minervo | |
| 40 | |
| 41 **FASTA reference** | |
| 42 This should be a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants | |
| 43 | |
| 44 ]]></help> | |
| 45 <citations> | |
| 46 <citation type="doi">10.1021/ja507164a</citation> | |
| 47 </citations> | |
| 48 </tool> | |
| 49 |