# HG changeset patch
# User jfb
# Date 1556400728 14400
# Node ID 1816bf5d17353570e3cd188275275b507143187a
# Parent  9e6f02d7d820ca1c2c7549052f80bc9eadceb824
Uploaded

diff -r 9e6f02d7d820 -r 1816bf5d1735 scoring function/KinatestScoring.xml
--- a/scoring function/KinatestScoring.xml	Sat Apr 27 17:02:02 2019 -0400
+++ b/scoring function/KinatestScoring.xml	Sat Apr 27 17:32:08 2019 -0400
@@ -7,24 +7,24 @@
         ln -s '$__tool_directory__/screener.csv' screener.csv &&
         ln -s '$FisherTable' Fisher-Char.csv && 
         ln -s '$CharacterizationTable' Fisher-Table.csv && 
-        Rscript '$__tool_directory__/KinatestFisherScoring.R' $outGroup $Ms $Mfi $Mfo $Mth $Mtw $Mo $Dz $Po $Ptw $Pth $Pfo $Pfi $Ps
+        Rscript '$__tool_directory__/KinatestFisherScoring.R' ${outGroup} ${Msix} ${Mfive} ${Mfour} ${Mthree} ${Mtwo} ${Mone} ${Dzero} ${Pone} ${Ptwo} ${Pthree} ${Pfour} ${Pfive} ${Psix}
     ]]></command>
     <inputs>
         <param format="csv" name="FisherTable" type="data" label="Fisher Odds Table output"/>
         <param format="csv" name="CharacterizationTable" type="data" label="Characterization Table Output"/>
-		<param name="Ms" type="text" value="ACD" label="Amino Acid(s) in -6 Position"/>
-		<param name="Mfi" type="text" value="EFG" label="Amino Acid(s) in -5 Position"/>
-		<param name="Mfo" type="text" value="HIK" label="Amino Acid(s) in -4 Position"/>
-		<param name="Mth" type="text" value="LMN" label="Amino Acid(s) in -3 Position"/>
-		<param name="Mtw" type="text" value="PQR" label="Amino Acid(s) in -2 Position"/>
-		<param name="Mo" type="text" value="STV" label="Amino Acid(s) in -1 Position"/>
-		<param name="Dz" type="text" value="Y" label="Amino Acid(s) in Central Position"/>
-		<param name="Po" type="text" value="VTS" label="Amino Acid(s) in +1 Position"/>
-		<param name="Ptw" type="text" value="RQP" label="Amino Acid(s) in +2 Position"/>
-		<param name="Pth" type="text" value="NML" label="Amino Acid(s) in +3 Position"/>
-		<param name="Pfo" type="text" value="KIH" label="Amino Acid(s) in +4 Position"/>
-		<param name="Pfi" type="text" value="GFE" label="Amino Acid(s) in +5 Position"/>
-		<param name="Ps" type="text" value="DCA" label="Amino Acid(s) in +6 Position"/>
+		<param name="Msix" type="text" value="ACD" label="Amino Acid(s) in -6 Position"/>
+		<param name="Mfive" type="text" value="EFG" label="Amino Acid(s) in -5 Position"/>
+		<param name="Mfour" type="text" value="HIK" label="Amino Acid(s) in -4 Position"/>
+		<param name="Mthree" type="text" value="LMN" label="Amino Acid(s) in -3 Position"/>
+		<param name="Mtwo" type="text" value="PQR" label="Amino Acid(s) in -2 Position"/>
+		<param name="Mone" type="text" value="STV" label="Amino Acid(s) in -1 Position"/>
+		<param name="Dzero" type="text" value="Y" label="Amino Acid(s) in Central Position"/>
+		<param name="Pone" type="text" value="VTS" label="Amino Acid(s) in +1 Position"/>
+		<param name="Ptwo" type="text" value="RQP" label="Amino Acid(s) in +2 Position"/>
+		<param name="Pthree" type="text" value="NML" label="Amino Acid(s) in +3 Position"/>
+		<param name="Pfour" type="text" value="KIH" label="Amino Acid(s) in +4 Position"/>
+		<param name="Pfive" type="text" value="GFE" label="Amino Acid(s) in +5 Position"/>
+		<param name="Psix" type="text" value="DCA" label="Amino Acid(s) in +6 Position"/>
 		<param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
     </inputs>      
     <outputs>