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comparison 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
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1:e0232cbac965 2:9227b8c3093b
1 <tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0"> 1 <tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0">
2 <description>for targeted resequencing data</description> 2 <description>for targeted resequencing data</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 4
5 picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext" 5 picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" --datatype "${input_file.ext}"
6 --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}" 6 --baitbed "${bait_bed}" --targetbed "${target_bed}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"
7 -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar" 7 -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar"
8 8
9 </command> 9 </command>
10 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> 10 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
11 <inputs> 11 <inputs>