--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/cgatools17/decodeCRR.xml	Wed Oct 21 10:09:15 2015 -0400
@@ -0,0 +1,78 @@
+<tool id="cg_decodecrr" name="DecodeCRR" version="1.7.1">
+
+	<description>retreives the sequence for a given range of a chromosome.</description> 
+
+	<requirements>		
+		<requirement type="package" version="1">cgatools17</requirement>
+	</requirements>
+
+	<command>
+		cgatools | head -1;
+		cgatools decodecrr 
+		#if $refcrr.reference == "custom":
+		--reference $refcrr.customcrr
+		#else:
+		--reference ${refcrr.reffile.fields.crr_path} 		 
+		#end if			
+		--output $output 
+		--range $range	
+	</command>
+
+	<inputs>
+		<conditional name="refcrr">
+			<param name="reference" type="select" label="Reference">
+				<option value="builtin" > Built-in Reference CRR </option>
+				<option value="custom"> Custom CRR file </option>						
+			</param>
+			<when value="builtin">
+				<param name="reffile" type="select" label="Reference">
+					<options from_data_table="cg_anno_files" />								
+				</param>
+			</when>
+			<when value="custom">
+				<param name="customcrr" type="data" format="crr" label="Select custom crr file" />
+			</when>
+		</conditional>
+
+		<param name="range" type="text" label="Select range" size="15" help="chr:begin-end e.g. chr4:30722030-30726957" />
+		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>			
+	</inputs>
+
+	<outputs>
+		<data format="txt" name="output" label="$fname ${tool.name} on ${on_string}"/>
+	</outputs>
+
+	<help> 
+	
+**What it does**
+
+Retrieves the sequence for a given range of a chromosome.
+
+**cgatools 1.7.1 Documentation**
+
+Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
+
+Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
+
+**Command line reference**::
+	
+COMMAND NAME
+    decodecrr - Prints the reference sequence for a given reference range.
+
+OPTIONS
+  -h [ --help ] 
+        Print this help message.
+
+  --reference arg
+        The reference crr file (may be passed in as argument at the end of the 
+        command).
+
+  --output arg (=STDOUT)
+        The output file (may be omitted for stdout).
+
+  --range arg
+        The range of bases to print (chr,begin,end or chr:begin-end).
+
+	</help>
+</tool>
+