diff TrackHub.py @ 46:061da5d3a219 draft

planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty

--- a/TrackHub.py	Tue May 01 21:52:46 2018 -0400
+++ b/TrackHub.py	Tue Jun 19 16:28:36 2018 -0400
@@ -51,10 +51,12 @@
         if Datatype.trackType == 'HTMLFeatures':
             self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
         self.logger = logging.getLogger(__name__)
+        self.nameIndexTrackList = []
 
-    
 
     def addTrack(self, trackDbObject):
+        if trackDbObject['nameIndex'] == "true":
+            self.nameIndexTracksList.append(trackDbObject['trackLabel'])
         if trackDbObject['dataType'].lower() == 'bam':
             subtools.add_track_json(self.trackList, trackDbObject['options'])
         elif trackDbObject['dataType'].lower() == 'bigwig':
@@ -104,7 +106,7 @@
         subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
 
     def _indexName(self):
-        subtools.generate_names(self.mySpecieFolderPath)
+        subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList)
         print "finished name index \n"
 
     def _outHtml(self):