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+ − 1 <tool id="bam_to_sam_parallel_unSQL" name="BAM to SAM (for DEA in parallel)" version="1.0.0">
+ − 2 <description>converts a list of BAM format files to SAM format (parallelized).</description>
+ − 3 <requirements>
+ − 4 <requirement type="package">samtools</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="python"> bam_to_sam_parallel_unSQL.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>
