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comparison testingXML/STKinamine.xml @ 1:89f54f2e28de draft

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author jfb
date Sun, 16 Sep 2018 14:36:46 -0400
parents 045d01edc59d
children 7882340aa21b
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0:045d01edc59d 1:89f54f2e28de
10 java -Djava.awt.headless=true -jar '$__tool_directory__/ST_KinaMine.jar' '$FDRreport' reference.fasta outputs $fdr output 10 java -Djava.awt.headless=true -jar '$__tool_directory__/ST_KinaMine.jar' '$FDRreport' reference.fasta outputs $fdr output
11 ]]></command> 11 ]]></command>
12 <inputs> 12 <inputs>
13 <param format="tabular" name="FDRreport" type="data" label="Distinct Peptide Report from S/T KALIP"/> 13 <param format="tabular" name="FDRreport" type="data" label="Distinct Peptide Report from S/T KALIP"/>
14 <param format="fasta" name="reference" type="data" label="Protein FASTA reference"/> 14 <param format="fasta" name="reference" type="data" label="Protein FASTA reference"/>
15 <param name="fdr" type="char" label="FDR"/> 15 <param name="fdr" type="character" label="FDR"/>
16 <param name="outGroup" type="text" value="kinase" label="Kinase Name"/> 16 <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
17 </inputs> 17 </inputs>
18 <outputs> 18 <outputs>
19 <data format="csv" name="Substrates" from_work_dir="outputs/output_Substrates.csv" label="${outGroup}_Substrates.csv"/> 19 <data format="csv" name="Substrates" from_work_dir="outputs/output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
20 <data format="csv" name="SBF" from_work_dir="outputs/output_SubBackFreq.csv" label="${outGroup}_SubstrateBackgroundFrequency.csv"/> 20 <data format="csv" name="SBF" from_work_dir="outputs/output_SubBackFreq.csv" label="${outGroup}_SubstrateBackgroundFrequency.csv"/>