Mercurial > repos > fcaramia > custom_amplicon_alignment

diff alignCustomAmplicon/alignCustomAmplicon_wrapper.xml @ 2:413ba6d9cc46 draft

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Uploaded
author fcaramia
date Wed, 09 Jan 2013 00:35:38 -0500
parents 6a1b222df393
children
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--- a/alignCustomAmplicon/alignCustomAmplicon_wrapper.xml	Wed Jan 09 00:27:53 2013 -0500
+++ b/alignCustomAmplicon/alignCustomAmplicon_wrapper.xml	Wed Jan 09 00:35:38 2013 -0500
@@ -8,6 +8,7 @@
   </requirements>
   <command interpreter="perl">
   	alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers 
+  	-j "\$JAVA_JAR_PATH/MergeSamFiles.jar"
   </command>
 
   <inputs>