comparison TrackHub.py @ 4:7e471cdd9e71 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 8d93b27353190eb23490c9480e560d84cb60c973

3:eda851e52060

class TrackHub:
    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData, jbrowse_host):
        self.input_files = inputFiles.tracks
        self.outfile = outputDirect
        self.outfolder = extra_files_path
        self.out_path = os.path.join(extra_files_path, genome)
        self.reference = reference
        self.tool_dir = tool_dir
        self.metaData = metaData
        self.raw = os.path.join(self.out_path, 'raw')
        self.json = os.path.join(self.out_path, 'json')

                metadata['style']['neg_color'] = "#005EFF"
        if 'category' not in metadata.keys() or metadata['category'] == '':
            metadata['category'] = "Default group"
        if track['dataType'] == 'blastxml':
            metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
        elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':
            metadata['type'] = "G-OnRamp_plugin/GenePred"
        else:
            metadata['type'] = "CanvasFeatures"

4:7e471cdd9e71

class TrackHub:
    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData, jbrowse_host):
        self.input_files = inputFiles.tracks
        self.outfile = outputDirect
        self.outfolder = extra_files_path
        self.out_path = os.path.join(extra_files_path, 'myHub')
        self.reference = reference
        self.tool_dir = tool_dir
        self.metaData = metaData
        self.raw = os.path.join(self.out_path, 'raw')
        self.json = os.path.join(self.out_path, 'json')

                metadata['style']['neg_color'] = "#005EFF"
        if 'category' not in metadata.keys() or metadata['category'] == '':
            metadata['category'] = "Default group"
        if track['dataType'] == 'blastxml':
            metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
        elif track['dataType'] == 'bigpsl':
            metadata['type'] = "G-OnRamp_plugin/BlatAlignment"
        elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':
            metadata['type'] = "G-OnRamp_plugin/GenePred"
        else:
            metadata['type'] = "CanvasFeatures"