comparison jbrowse.py @ 27:61ce21e36cb5 draft

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

26:08776ba76cf5

            trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'

        trackType = 'JBrowse/View/Track/CanvasFeatures'
        if 'trackType' in gffOpts:
            trackType = gffOpts['trackType']
        trackData['trackType'] = trackType

        if trackType == 'JBrowse/View/Track/CanvasFeatures':
            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']

        self._add_track_json(trackData)

        if gffOpts.get('index', 'false') == 'true':
            self.tracksToIndex.append("%s" % trackData['label'])

        viz_data.update(generalData)
        self._add_json(viz_data)

        if 'GCContent' in data['plugins_python']:
            self._add_track_json({
                "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta",
                "type": "GCContent/View/Track/GCContentXY",
                "label": "GC Content",
                "key": "GCContentXY",
                "urlTemplate": "seq/genome.fasta",
                "bicolor_pivot": 0.5,

                    "metadata_dbkey": "",
                }
                # TODO: Expose params for everyone.
            })
            self._add_track_json({
                "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta",
                "type": "GCContent/View/Track/GCContentXY",
                "label": "GC skew",
                "key": "GCSkew",
                "urlTemplate": "seq/genome.fasta",
                "gcMode": "skew",

27:61ce21e36cb5

            trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'

        trackType = 'JBrowse/View/Track/CanvasFeatures'
        if 'trackType' in gffOpts:
            trackType = gffOpts['trackType']
        trackData['type'] = trackType
        trackData['trackType'] = trackType  # Probably only used by old jbrowse versions

        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)

        if gffOpts.get('index', 'false') == 'true':
            self.tracksToIndex.append("%s" % trackData['label'])

        viz_data.update(generalData)
        self._add_json(viz_data)

        if 'GCContent' in data['plugins_python']:
            self._add_track_json({
                "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
                "type": "GCContent/View/Track/GCContentXY",
                "label": "GC Content",
                "key": "GCContentXY",
                "urlTemplate": "seq/genome.fasta",
                "bicolor_pivot": 0.5,

                    "metadata_dbkey": "",
                }
                # TODO: Expose params for everyone.
            })
            self._add_track_json({
                "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
                "type": "GCContent/View/Track/GCContentXY",
                "label": "GC skew",
                "key": "GCSkew",
                "urlTemplate": "seq/genome.fasta",
                "gcMode": "skew",