# HG changeset patch
# User jfb
# Date 1519247533 18000
# Node ID 3a3953801f5e3a175b78de56afa0ba2dfdfd97f4
# Parent  e8b02855fe62c08266594719f661410813c9502d
Uploaded

diff -r e8b02855fe62 -r 3a3953801f5e zippable Kinamine/KinaMine.jar
Binary file zippable Kinamine/KinaMine.jar has changed
diff -r e8b02855fe62 -r 3a3953801f5e zippable Kinamine/Kinamine.xml
--- 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>
diff -r e8b02855fe62 -r 3a3953801f5e zippable Kinamine/test-data/outputoutput_Substrate Background Frequency.csv
Binary file zippable Kinamine/test-data/outputoutput_Substrate Background Frequency.csv has changed
diff -r e8b02855fe62 -r 3a3953801f5e zippable Kinamine/test-data/outputoutput_Substrates.csv
Binary file zippable Kinamine/test-data/outputoutput_Substrates.csv has changed