--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/bam_to_sam_parallel.xml	Mon May 13 10:06:30 2013 -0400
@@ -0,0 +1,32 @@
+<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>