--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyCheckGTFfile.xml	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,53 @@
+ <tool id ="pyCheckGTFfile" name="pyCheckGTFfile">
+	<requirements>
+        	<requirement type="package">pyCRAC</requirement>
+    	</requirements>
+	<command interpreter="python"> 
+	/usr/local/bin/pyCheckGTFfile.py --gtf $addGTF.gtf -o $out
+	</command>
+	<version_command>/usr/local/bin/pyCheckGTFfile.py --version</version_command>
+	<inputs>
+		<conditional name="addGTF">
+			<param name="gtfFile" type="select"  label="Choose GTF File from">
+				<option value="default" selected="true">Defaults</option>
+				<option value="other">History</option>
+			</param>	
+			<when value="default">
+				<param name="gtf" type="select"  label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
+					<options from_data_table="pycrac_gtf"/>
+				</param>
+			</when>
+			<when value="other">
+				<param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
+			</when>
+		</conditional>
+		<param name="label" type="text" format="txt" size="30" value="pyCheckGTFfile" label="Enter output file label -o" />
+	</inputs>
+
+	<outputs>
+		<data format="gtf" name="out" label="${label.value}.gtf"/>
+	</outputs>
+	<help>
+.. class:: infomark
+
+**pyCheckGTFfile**
+
+pyCheckGTFfile is part of the pyCRAC_ package. Renames duplicated gene names in your GTF annotation file.
+
+.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
+        
+------
+
+**Parameter list**
+
+Options::
+
+  --gtf=gtf input file
+                        type the path to the gtf file that you want to use.
+  -o FILE, --output=FILE
+                        Optional. Specify the name of the output file. Default
+                        is standard output. Make sure it has the .gtf
+                        extension!
+
+	</help>
+</tool>