--- a/SMART/galaxy/CompareOverlappingSmallQuery.xml	Thu Mar 14 05:25:40 2013 -0400
+++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml	Thu Mar 14 05:37:08 2013 -0400
@@ -33,13 +33,24 @@
 		#if $OptionDistance.Dist == 'Yes':
 			-d $OptionDistance.distance
 		#end if
-		#if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
+		#if $OptionMinOverlap.present == 'Yes':
+			-m $OptionMinOverlap.minOverlap
+		#end if
+		#if $OptionPcOverlapQuery.present == 'Yes':
+			-p $OptionPcOverlapQuery.minOverlap
+		#end if
+		#if $OptionPcOverlapRef.present == 'Yes':
+			-P $OptionPcOverlapRef.minOverlap
+		#end if
+		#if $OptionCollinearOrAntiSens.OptionCA == 'Collinear':
 			-c 
-		#elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
+		#elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
 			-a
 		#end if	
 		$InvertMatch
 		$NotOverlapping
+		$OptionInclusionQuery
+		$OptionInclusionRef
 	</command>
 
 	<inputs>
@@ -111,13 +122,48 @@
 			<when value="No">
 			</when>
 		</conditional>
-		<conditional name="OptionColinearOrAntiSens">
-			<param name="OptionCA" type="select" label="Colinear or anti-sens">
-				<option value="Colinear">Colinear</option>
+		<conditional name="OptionMinOverlap">
+			<param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="minOverlap" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		<conditional name="OptionPcOverlapQuery">
+			<param name="present" type="select" label="N% of the query must overlap">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="minOverlap" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		<conditional name="OptionPcOverlapRef">
+			<param name="present" type="select" label="N% of the reference must overlap">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="minOverlap" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		<param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must nested in a query"/>
+		<param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must nested in a query"/>
+		<conditional name="OptionCollinearOrAntiSens">
+			<param name="OptionCA" type="select" label="Collinear or anti-sens">
+				<option value="Collinear">Collinear</option>
 				<option value="AntiSens">AntiSens</option>
 				<option value="NONE" selected="true">NONE</option>
 			</param>
-			<when value="Colinear">
+			<when value="Collinear">
 			</when>
 			<when value="AntiSens">
 			</when>