--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RNASeQC.xml	Fri Jul 12 15:42:06 2013 -0500
@@ -0,0 +1,27 @@
+<tool id="RNASeQC" name="RNASeQC">
+	<description>RNASeQC: Quality control metrics for RNA-seq data</description>
+	<requirements>
+		<requirement type="package" version="0.6.2">bwa</requirement>
+		<requirement type="set_environment">RNASEQPATH</requirement>
+	</requirements>
+	<command interpreter="java">
+-jar \$RNASEQCPATH/RNASeQC.jar -r $input1 -t $input2 -s "SampleID|$input3|Notes" -o output
+	</command>
+
+	<inputs>
+
+	  	<param name="input1" type="data" format="fasta" label="Reference genome"/>
+		<param name="input2" type="data" format="gtf" label="File Defining transcipts"/>
+		<param name="input4" type="data" format="bam" label="BAM File"/>
+
+	</inputs>
+
+	<outputs>
+		<data format="txt" name="output" label="output file" />
+    	</outputs>
+
+  <help>
+This tool computes GC content from a FASTA file.
+  </help>
+
+</tool>