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diff rgPicardHsMetrics.xml @ 2:9227b8c3093b

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Updated command line format per dev team standards.
author devteam <devteam@galaxyproject.org>
date Tue, 02 Apr 2013 09:42:36 -0400
parents 1cd7f3b42609
children
line wrap: on
line diff
--- a/rgPicardHsMetrics.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/rgPicardHsMetrics.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,8 +2,8 @@
   <description>for targeted resequencing data</description>
   <command interpreter="python">
 
-    picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext"
-    --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}"
+    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" --datatype "${input_file.ext}"
+    --baitbed "${bait_bed}" --targetbed "${target_bed}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"
     -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar"
 
   </command>