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comparison 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
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1:e0232cbac965 2:9227b8c3093b
1 <tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0"> 1 <tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0">
2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> 2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
3 <command interpreter="python"> 3 <command interpreter="python">
4 picard_wrapper.py 4 picard_wrapper.py
5 --input "$input_file" 5 --input "${input_file}"
6 --bai-file "$input_file.metadata.bam_index" 6 --bai-file "${input_file.metadata.bam_index}"
7 -t "$htmlfile" 7 -t "${htmlfile}"
8 -d "$htmlfile.files_path" 8 -d "${htmlfile.files_path}"
9 -j "\$JAVA_JAR_PATH/BamIndexStats.jar" 9 -j "\$JAVA_JAR_PATH/BamIndexStats.jar"
10 --tmpdir "${__new_file_path__}" 10 --tmpdir "${__new_file_path__}"
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for" 13 <param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for"