Repository 's_mart'
hg clone https://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart

Changeset 64:783e6ed4eb66 (2015-10-19)
Previous changeset 63:5f210bc9f486 (2015-10-19) Next changeset 66:090709ab81d1 (2015-11-04)
Commit message:
Minor bug correction. Added casts to str in Galaxy XML files. Also closed the writer in the Python script "changeTagName."
modified:
SMART/Java/Python/changeTagName.py
SMART/galaxy/CompareOverlappingAdapt.xml
SMART/galaxy/CompareOverlappingSmallQuery.xml
SMART/galaxy/CompareOverlappingSmallRef.xml
b
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
b
@@ -83,6 +83,7 @@
     parser.transcriptListParser.close()
 
     writer.write()
+    writer.close()
 
     if options.mysql:
         mysqlWriter.write()
b
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
b
@@ -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>
b
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
b
@@ -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>
b
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
b
@@ -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>