comparison Bam.py @ 26:df42241d3731 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty

25:99dad5f9444c

        # TODO: Think about how to avoid repetition of the color treatment
        self.track_color = self.data_bam["track_color"]

        # TODO: Think about how to avoid repetition of the group_name everywhere
        self.group_name = self.data_bam["group_name"]
        if self.data_bam["long_label"]:
            self.long_label = self.data_bam["long_label"]
        else:
            self.long_label = self.name_bam
        # First: Add the bam file

        self.createTrack(file_path=self.name_bam,
                         track_name=self.name_bam,
                         long_label=self.long_label, track_type='bam', visibility='pack', priority=self.priority,
                         track_file=bam_index_file_path,
                         track_color=self.track_color,
                         group_name=self.group_name
                         )
        #
        # dataURL = "tracks/%s" % self.name_bam
        #
        # trackDb = TrackDb(

26:df42241d3731

        # TODO: Think about how to avoid repetition of the color treatment
        self.track_color = self.data_bam["track_color"]

        # TODO: Think about how to avoid repetition of the group_name everywhere
        self.group_name = self.data_bam["group_name"]
        self.database = self.data_bam["database"]
        if self.data_bam["long_label"]:
            self.long_label = self.data_bam["long_label"]
        else:
            self.long_label = self.name_bam
        # First: Add the bam file

        self.createTrack(file_path=self.name_bam,
                         track_name=self.name_bam,
                         long_label=self.long_label, track_type='bam', visibility='pack', priority=self.priority,
                         track_file=bam_index_file_path,
                         track_color=self.track_color,
                         group_name=self.group_name,
                         database=self.database
                         )
        #
        # dataURL = "tracks/%s" % self.name_bam
        #
        # trackDb = TrackDb(