Mercurial > repos > devteam > picard
comparison rgPicardHsMetrics.xml @ 2:9227b8c3093b
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 |
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| 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> |