Mercurial > repos > iuc > jbrowse

comparison jbrowse.py @ 27:61ce21e36cb5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
author iuc
date Wed, 20 Feb 2019 11:50:21 -0500
parents 1cfc579079a6
children d0743cb18ed8
comparison
equal deleted inserted replaced
26:08776ba76cf5 27:61ce21e36cb5
641 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments' 641 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
642 642
643 trackType = 'JBrowse/View/Track/CanvasFeatures' 643 trackType = 'JBrowse/View/Track/CanvasFeatures'
644 if 'trackType' in gffOpts: 644 if 'trackType' in gffOpts:
645 trackType = gffOpts['trackType'] 645 trackType = gffOpts['trackType']
646 trackData['trackType'] = trackType 646 trackData['type'] = trackType
647 647 trackData['trackType'] = trackType # Probably only used by old jbrowse versions
648 if trackType == 'JBrowse/View/Track/CanvasFeatures': 648
649 if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
649 if 'transcriptType' in gffOpts and gffOpts['transcriptType']: 650 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
650 trackData['transcriptType'] = gffOpts['transcriptType'] 651 trackData['transcriptType'] = gffOpts['transcriptType']
651 if 'subParts' in gffOpts and gffOpts['subParts']: 652 if 'subParts' in gffOpts and gffOpts['subParts']:
652 trackData['subParts'] = gffOpts['subParts'] 653 trackData['subParts'] = gffOpts['subParts']
653 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']: 654 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
654 trackData['impliedUTRs'] = gffOpts['impliedUTRs'] 655 trackData['impliedUTRs'] = gffOpts['impliedUTRs']
656 elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
657 if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
658 trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']
655 659
656 self._add_track_json(trackData) 660 self._add_track_json(trackData)
657 661
658 if gffOpts.get('index', 'false') == 'true': 662 if gffOpts.get('index', 'false') == 'true':
659 self.tracksToIndex.append("%s" % trackData['label']) 663 self.tracksToIndex.append("%s" % trackData['label'])
818 viz_data.update(generalData) 822 viz_data.update(generalData)
819 self._add_json(viz_data) 823 self._add_json(viz_data)
820 824
821 if 'GCContent' in data['plugins_python']: 825 if 'GCContent' in data['plugins_python']:
822 self._add_track_json({ 826 self._add_track_json({
823 "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta", 827 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
824 "type": "GCContent/View/Track/GCContentXY", 828 "type": "GCContent/View/Track/GCContentXY",
825 "label": "GC Content", 829 "label": "GC Content",
826 "key": "GCContentXY", 830 "key": "GCContentXY",
827 "urlTemplate": "seq/genome.fasta", 831 "urlTemplate": "seq/genome.fasta",
828 "bicolor_pivot": 0.5, 832 "bicolor_pivot": 0.5,
837 "metadata_dbkey": "", 841 "metadata_dbkey": "",
838 } 842 }
839 # TODO: Expose params for everyone. 843 # TODO: Expose params for everyone.
840 }) 844 })
841 self._add_track_json({ 845 self._add_track_json({
842 "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta", 846 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
843 "type": "GCContent/View/Track/GCContentXY", 847 "type": "GCContent/View/Track/GCContentXY",
844 "label": "GC skew", 848 "label": "GC skew",
845 "key": "GCSkew", 849 "key": "GCSkew",
846 "urlTemplate": "seq/genome.fasta", 850 "urlTemplate": "seq/genome.fasta",
847 "gcMode": "skew", 851 "gcMode": "skew",