Mercurial > repos > iuc > jbrowse

diff jbrowse.py @ 14:18be2d72fdee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
author iuc
date Thu, 08 Jun 2017 17:31:38 -0400
parents 69c5e9c0add0
children b5c5470d7c09
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line diff
--- a/jbrowse.py	Thu Feb 09 12:36:16 2017 -0500
+++ b/jbrowse.py	Thu Jun 08 17:31:38 2017 -0400
@@ -472,6 +472,11 @@
             "storeClass": "JBrowse/Store/SeqFeature/BAM",
         })
 
+        # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
+        # So remove the default 'feature' value for these bam tracks
+        if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
+            del trackData['style']['className']
+
         self._add_track_json(trackData)
 
         if bamOpts.get('auto_snp', 'false') == 'true':