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author | devteam |
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date | Thu, 20 Feb 2014 13:39:10 -0500 |
parents | fda8c1757585 |
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<tool name="Sort Sam" id="picard_SortSam" version="1.106.0"> <!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml --> <!-- warning: the sam format output doesn't work. TODO: fix it --> <description>Sorts SAM or BAM file</description> <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> <command interpreter="python"> picard_wrapper.py --input "$inputFile" -s "$sort_order" -o "$outFile" --output-format $outputFormat -j "\$JAVA_JAR_PATH/SortSam.jar" </command> <inputs> <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted" help="If empty, upload or import a SAM/BAM dataset." /> <param name="sort_order" type="select" label="Sort order"> <option value="coordinate" selected="True">coordinate</option> <option value="queryname">queryname</option> <option value="unsorted">unsorted</option> </param> <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" /> </inputs> <outputs> <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat}" /> <change_format> <when input="outputFormat" value="sam" format="sam" /> </change_format> </outputs> <help> SortSam USAGE: SortSam [options] Documentation: http://picard.sourceforge.net/command-line-overview.shtml#SortSam Sorts the input SAM or BAM. Input and output formats are determined by file extension. Option Description INPUT=File The BAM or SAM file to sort. Required. OUTPUT=File The sorted BAM or SAM output file. Required. SORT_ORDER=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} </help> </tool>