# HG changeset patch
# User m-zytnicki
# Date 1363253855 14400
# Node ID 5a054da778088ef163c7026a7ea9752254fe4d93
# Parent 2da30502c2f11cc59c6484459beb52955fbc07f9
Updated CompareOverlappingSmallRef.xml
diff -r 2da30502c2f1 -r 5a054da77808 SMART/galaxy/CompareOverlappingSmallRef.xml
--- a/SMART/galaxy/CompareOverlappingSmallRef.xml Thu Mar 14 05:37:08 2013 -0400
+++ b/SMART/galaxy/CompareOverlappingSmallRef.xml Thu Mar 14 05:37:35 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
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