# HG changeset patch
# User yating-l
# Date 1526355031 14400
# Node ID 8886033b4f84e620353ddbf7df2834bc579c835b
# Parent  e2ebf58c906857cca92eaef63e0059a8b15f60f7
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 4e8e5448a54f794bced67046e236988031616180

diff -r e2ebf58c9068 -r 8886033b4f84 datatypes/interval/BigPsl.py
--- a/datatypes/interval/BigPsl.py	Mon May 14 21:37:50 2018 -0400
+++ b/datatypes/interval/BigPsl.py	Mon May 14 23:30:31 2018 -0400
@@ -26,7 +26,7 @@
     def initSettings(self):
         super(BigPsl, self).initSettings()
         self.extraSettings["glyph"] = "JBrowse/View/FeatureGlyph/Segments"  
-        #self.extraSettings["subfeatureClasses"] = "match_part"
+
 
     def validateData(self):
         self.validateOptions = self.getValidateOptions(tab="True", autoSql=self.autoSql)
diff -r e2ebf58c9068 -r 8886033b4f84 jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Mon May 14 21:37:50 2018 -0400
+++ b/jbrowseArchiveCreator.xml	Mon May 14 23:30:31 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.3">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.4">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
     </description>
diff -r e2ebf58c9068 -r 8886033b4f84 tracks/CanvasFeatures.py
--- a/tracks/CanvasFeatures.py	Mon May 14 21:37:50 2018 -0400
+++ b/tracks/CanvasFeatures.py	Mon May 14 23:30:31 2018 -0400
@@ -26,10 +26,10 @@
         if self.dataType == 'gff':
             # need .gff3.gz extension to index the name of the track with generate-name.pl
             track['urlTemplate'] = os.path.join('tracks', self.trackName + '.gff3.gz')
-            # needed to show match_part in Blat and Blast alignment as subfeatures
-            track['glyph'] = "JBrowse/View/FeatureGlyph/Segments"
         else:
             track['urlTemplate'] = os.path.join('tracks', self.trackName)
+        if 'glyph' in self.extraSettings:
+            track['glyph'] = self.extraSettings['glyph']
         if 'subfeatureClasses' in self.extraSettings:
             track['subfeatureClasses'] = self.extraSettings['subfeatureClasses']
         track['label'] = self.trackLabel