# HG changeset patch
# User m-zytnicki
# Date 1366209575 14400
# Node ID 03045debed6e8490b7ca66905d228e6bcd5f069a
# Parent  5a054da778088ef163c7026a7ea9752254fe4d93
Uploaded

diff -r 5a054da77808 -r 03045debed6e SMART/galaxy/CompareOverlappingSmallQuery.xml
--- a/SMART/galaxy/CompareOverlappingSmallQuery.xml	Thu Mar 14 05:37:35 2013 -0400
+++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml	Wed Apr 17 10:39:35 2013 -0400
@@ -36,21 +36,13 @@
 		#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 $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
+		#elif $OptionCollinearOrAntiSens.OptionCA == 'Antisense':
 			-a
 		#end if	
 		$InvertMatch
 		$NotOverlapping
-		$OptionInclusionQuery
-		$OptionInclusionRef
 	</command>
 
 	<inputs>
@@ -112,7 +104,7 @@
 			</when>
 		</conditional>
 		<conditional name="OptionDistance">
-			<param name="Dist" type="select" label="Maximum Distance between two reads">
+			<param name="Dist" type="select" label="Maximum Distance between two regions">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -133,45 +125,21 @@
 			<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">
+			<param name="OptionCA" type="select" label="Collinear or Antisense">
 				<option value="Collinear">Collinear</option>
-				<option value="AntiSens">AntiSens</option>
+				<option value="Antisense">Antisense</option>
 				<option value="NONE" selected="true">NONE</option>
 			</param>
 			<when value="Collinear">
 			</when>
-			<when value="AntiSens">
+			<when value="Antisense">
 			</when>
 			<when value="NONE">
 			</when>
 		</conditional>
 		<param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
-		<param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
+		<param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by default."/>
 	</inputs>
 
 	<outputs>