<tool id="bam_to_sam_parallel" name="BAM to SAM (for DEA)" 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>