Mercurial > repos > jfb > kinamine
changeset 7:3a3953801f5e draft
Uploaded
| author | jfb |
|---|---|
| date | Wed, 21 Feb 2018 16:12:13 -0500 |
| parents | e8b02855fe62 |
| children | 2749290604f4 |
| files | zippable Kinamine/KinaMine.jar zippable Kinamine/Kinamine.xml zippable Kinamine/test-data/outputoutput_Substrate Background Frequency.csv zippable Kinamine/test-data/outputoutput_Substrates.csv |
| diffstat | 4 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/zippable Kinamine/Kinamine.xml Wed Feb 21 12:42:54 2018 -0500 +++ b/zippable Kinamine/Kinamine.xml Wed Feb 21 16:12:13 2018 -0500 @@ -3,9 +3,12 @@ <requirements> <requirement type="package" version="8.0.1440.1">Java</requirement> </requirements> +<!-- + java -Djava.awt.headless=true -cp KinaMine.jar KinaMine.KinaMine FDRreport.txt reference.fasta $test KINASE +--> <command><![CDATA[ mkdir -p output && - java -Djava.awt.headless=true -cp '$__tool_directory__/Kinamine.jar' kinamine.KinaMine $FDRreport $reference output $fdr + java -Djava.awt.headless=true -cp '$__tool_directory__/Kinamine.jar' KinaMine.KinaMine $FDRreport $reference output $fdr ]]></command> <inputs> <param format="txt" name="FDRreport" type="data" label="Distinct Peptide Report"/> @@ -14,8 +17,8 @@ <param name="outGroup" type="text" value= "kinase" label="Kinase Name"/> </inputs> <outputs> - <data format="csv" name="Substrates" from_work_dir="output_Substrates.csv" label="${outGroup}_Substrates.csv"/> - <data format="csv" name="SBF" from_work_dir="output2_Substrate Background Frequency.csv" label="$[outGroup]_Substrate Background Frequency"/> + <data format="csv" name="Substrates" from_work_dir="outputoutput_Substrates.csv" label="${outGroup}_Substrates.csv"/> + <data format="csv" name="SBF" from_work_dir="outputoutput_Substrate Background Frequency.csv" label="$[outGroup]_Substrate Background Frequency"/> </outputs> <tests> <test>