Mercurial > repos > yufei-luo > s_mart
comparison SMART/DiffExpAnal/bam_to_sam_parallel.xml @ 31:0ab839023fe4
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 14:33:21 -0400 |
| parents | 94ab73e8a190 |
| children |
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| 30:5677346472b5 | 31:0ab839023fe4 |
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| 1 <tool id="bam_to_sam_parallel" name="BAM to SAM (for DEA)" version="1.0.0"> | |
| 2 <description>converts a list of BAM format files to SAM format.</description> | |
| 3 <requirements> | |
| 4 <requirement type="package">samtools</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> bam_to_sam_parallel.py | |
| 7 --input1=$input1 | |
| 8 --output1=$output1 | |
| 9 $header | |
| 10 $tar $outputTarFile | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <param name="input1" type="data" format="txt" label="BAM File LIST to Convert" /> | |
| 14 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> | |
| 15 <param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." /> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="txt" name="output1" label="converted SAM LIST files " /> | |
| 19 <data name="outputTarFile" format="tar"> | |
| 20 <filter>tar</filter> | |
| 21 </data> | |
| 22 </outputs> | |
| 23 <help> | |
| 24 | |
| 25 **What it does** | |
| 26 | |
| 27 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. | |
| 28 | |
| 29 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | |
| 30 | |
| 31 </help> | |
| 32 </tool> |