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diff picard_SortSam.xml @ 43:c810e9bc55af draft

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author devteam
date Thu, 13 Feb 2014 22:14:53 -0500
parents 70c2d93ea217
children
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--- a/picard_SortSam.xml	Thu Feb 13 22:02:05 2014 -0500
+++ b/picard_SortSam.xml	Thu Feb 13 22:14:53 2014 -0500
@@ -1,13 +1,13 @@
 <tool name="Sort Sam" id="picard_SortSam" version="1.106.0">
 <!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml -->
-  <requirements><requirement type="package">picard</requirement></requirements>
+  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
       --input "$inputFile"
       -s "$sort_order"
       -o "$outFile"
       --output-format $outputFormat
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SortSam.jar"
+      -j "\$JAVA_JAR_PATH/SortSam.jar"
   </command>
   <inputs>
     <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted"