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comparison picard_ReplaceSamHeader.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 3d4f1fa26f0e
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1:e0232cbac965 2:9227b8c3093b
1 <tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0"> 1 <tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" 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 "$inputFile" 5 --input "${inputFile}"
6 -o $outFile 6 -o "${outFile}"
7 --header-file $headerFile 7 --header-file "${headerFile}"
8 --output-format $outputFormat 8 --output-format "${outputFormat}"
9 -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar" 9 -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar"
10 --tmpdir "${__new_file_path__}" 10 --tmpdir "${__new_file_path__}"
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)" 13 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)"