Mercurial > repos > devteam > picard
comparison rgPicardFixMate.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="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0"> | 1 <tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0"> |
| 2 <description>for paired data</description> | 2 <description>for paired data</description> |
| 3 <command interpreter="python"> | 3 <command interpreter="python"> |
| 4 picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" | 4 picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}" |
| 5 --output-format "$outputFormat" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "$sortOrder" | 5 --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}" |
| 6 </command> | 6 </command> |
| 7 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | 7 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> |
| 8 <inputs> | 8 <inputs> |
| 9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix" | 9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix" |
| 10 help="If empty, upload or import a SAM/BAM dataset."/> | 10 help="If empty, upload or import a SAM/BAM dataset."/> |