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comparison picard_SortSam.xml @ 43:c810e9bc55af draft

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author devteam
date Thu, 13 Feb 2014 22:14:53 -0500
parents 70c2d93ea217
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42:c25cd3e674a5 43:c810e9bc55af
1 <tool name="Sort Sam" id="picard_SortSam" version="1.106.0"> 1 <tool name="Sort Sam" id="picard_SortSam" version="1.106.0">
2 <!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml --> 2 <!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml -->
3 <requirements><requirement type="package">picard</requirement></requirements> 3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
4 <command interpreter="python"> 4 <command interpreter="python">
5 picard_wrapper.py 5 picard_wrapper.py
6 --input "$inputFile" 6 --input "$inputFile"
7 -s "$sort_order" 7 -s "$sort_order"
8 -o "$outFile" 8 -o "$outFile"
9 --output-format $outputFormat 9 --output-format $outputFormat
10 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SortSam.jar" 10 -j "\$JAVA_JAR_PATH/SortSam.jar"
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted" 13 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted"
14 help="If empty, upload or import a SAM/BAM dataset." /> 14 help="If empty, upload or import a SAM/BAM dataset." />
15 <param name="sort_order" type="select" label="Sort order"> 15 <param name="sort_order" type="select" label="Sort order">