diff jbrowse.py @ 27:61ce21e36cb5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46

--- a/jbrowse.py	Tue Feb 19 15:43:37 2019 -0500
+++ b/jbrowse.py	Wed Feb 20 11:50:21 2019 -0500
@@ -643,15 +643,19 @@
         trackType = 'JBrowse/View/Track/CanvasFeatures'
         if 'trackType' in gffOpts:
             trackType = gffOpts['trackType']
-        trackData['trackType'] = trackType
+        trackData['type'] = trackType
+        trackData['trackType'] = trackType  # Probably only used by old jbrowse versions
 
-        if trackType == 'JBrowse/View/Track/CanvasFeatures':
+        if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
             if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
                 trackData['transcriptType'] = gffOpts['transcriptType']
             if 'subParts' in gffOpts and gffOpts['subParts']:
                 trackData['subParts'] = gffOpts['subParts']
             if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
                 trackData['impliedUTRs'] = gffOpts['impliedUTRs']
+        elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
+            if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
+                trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']
 
         self._add_track_json(trackData)
 
@@ -820,7 +824,7 @@
 
         if 'GCContent' in data['plugins_python']:
             self._add_track_json({
-                "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta",
+                "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
                 "type": "GCContent/View/Track/GCContentXY",
                 "label": "GC Content",
                 "key": "GCContentXY",
@@ -839,7 +843,7 @@
                 # TODO: Expose params for everyone.
             })
             self._add_track_json({
-                "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta",
+                "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
                 "type": "GCContent/View/Track/GCContentXY",
                 "label": "GC skew",
                 "key": "GCSkew",