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view deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/bam_to_sam_parallel.xml @ 10:6e573fd3c41b draft
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author | yufei-luo |
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date | Mon, 13 May 2013 10:06:30 -0400 |
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<tool id="bam_to_sam_parallel" name="BAM to SAM" version="1.0.0"> <description>converts a list of BAM format files to SAM format</description> <requirements> <requirement type="package">samtools</requirement> </requirements> <command interpreter="python"> bam_to_sam_parallel.py --input1=$input1 --output1=$output1 $header $tar $outputTarFile </command> <inputs> <param name="input1" type="data" format="txt" label="BAM File LIST to Convert" /> <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> <param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." /> </inputs> <outputs> <data format="txt" name="output1" label="converted SAM LIST files " /> <data name="outputTarFile" format="tar"> <filter>tar</filter> </data> </outputs> <help> **What it does** This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml </help> </tool>