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diff picard_BamIndexStats.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/picard_BamIndexStats.xml	Thu Oct 25 12:51:42 2012 -0400
+++ b/picard_BamIndexStats.xml	Tue Apr 02 09:42:36 2013 -0400
@@ -2,10 +2,10 @@
   <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
   <command interpreter="python">
     picard_wrapper.py
-      --input "$input_file"
-      --bai-file "$input_file.metadata.bam_index"
-      -t "$htmlfile"
-      -d "$htmlfile.files_path"
+      --input "${input_file}"
+      --bai-file "${input_file.metadata.bam_index}"
+      -t "${htmlfile}"
+      -d "${htmlfile.files_path}"
       -j "\$JAVA_JAR_PATH/BamIndexStats.jar"
       --tmpdir "${__new_file_path__}" 
   </command>