# HG changeset patch
# User m-zytnicki
# Date 1445257004 -7200
# Node ID 783e6ed4eb664e638e4fdd8d717ee11e28599df0
# Parent  5f210bc9f486eb967d8f1e8566da8d046f4cdc92
Minor bug correction.
Added casts to str in Galaxy XML files.  Also closed the writer in the Python script "changeTagName."

diff -r 5f210bc9f486 -r 783e6ed4eb66 SMART/Java/Python/changeTagName.py
--- a/SMART/Java/Python/changeTagName.py	Mon Oct 19 12:02:29 2015 +0200
+++ b/SMART/Java/Python/changeTagName.py	Mon Oct 19 14:16:44 2015 +0200
@@ -83,6 +83,7 @@
     parser.transcriptListParser.close()
 
     writer.write()
+    writer.close()
 
     if options.mysql:
         mysqlWriter.write()
diff -r 5f210bc9f486 -r 783e6ed4eb66 SMART/galaxy/CompareOverlappingAdapt.xml
--- a/SMART/galaxy/CompareOverlappingAdapt.xml	Mon Oct 19 12:02:29 2015 +0200
+++ b/SMART/galaxy/CompareOverlappingAdapt.xml	Mon Oct 19 14:16:44 2015 +0200
@@ -8,9 +8,9 @@
 		#if $OptionDistance.Dist == 'Yes':
 			-d $OptionDistance.distance
 		#end if
-		#if $OptionCA == 'Collinear':
+		#if str($OptionCA) == 'Collinear':
 			-c 
-		#elif $OptionCA == 'AntiSense':
+		#elif str($OptionCA) == 'AntiSense':
 			-a
 		#end if	
 	</command>
diff -r 5f210bc9f486 -r 783e6ed4eb66 SMART/galaxy/CompareOverlappingSmallQuery.xml
--- a/SMART/galaxy/CompareOverlappingSmallQuery.xml	Mon Oct 19 12:02:29 2015 +0200
+++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml	Mon Oct 19 14:16:44 2015 +0200
@@ -14,9 +14,9 @@
 		#if $OptionPcOverlapRef.present == 'Yes':
 			-P $OptionPcOverlapRef.minOverlap
 		#end if
-		#if $OptionCA == 'Collinear':
+		#if str($OptionCA) == 'Collinear':
 			-c 
-		#elif $OptionCA == 'AntiSense':
+		#elif str($OptionCA) == 'AntiSense':
 			-a
 		#end if	
 	</command>
diff -r 5f210bc9f486 -r 783e6ed4eb66 SMART/galaxy/CompareOverlappingSmallRef.xml
--- a/SMART/galaxy/CompareOverlappingSmallRef.xml	Mon Oct 19 12:02:29 2015 +0200
+++ b/SMART/galaxy/CompareOverlappingSmallRef.xml	Mon Oct 19 14:16:44 2015 +0200
@@ -14,9 +14,9 @@
 		#if $OptionPcOverlapRef.present == 'Yes':
 			-P $OptionPcOverlapRef.minOverlap
 		#end if
-		#if $OptionCA == 'Collinear':
+		#if str($OptionCA) == 'Collinear':
 			-c 
-		#elif $OptionCA == 'AntiSense':
+		#elif str($OptionCA) == 'AntiSense':
 			-a
 		#end if	
 	</command>