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comparison rgPicardFixMate.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="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."/>