comparison jbrowse2.py @ 6:79f7265f90bd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9-dirty

5:efc64d8f4b72

        # We need to know the track type from the config.json generated just before
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)

        for track_conf in self.tracksToAdd:  # config_json["tracks"]:
            track_types[track_conf["trackId"]] = track_conf["type"]

        for on_track in data["visibility"]["default_on"]:
            style_data = {"type": "LinearBasicDisplay", "height": 100}
            if on_track in data["style"]:

                start = int(loc_match.group(2))
                end = int(loc_match.group(3))
        elif self.genome_name is not None:
            refName = self.genome_name
            start = 0
            end = 1000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708

        if refName is not None:
            # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
            view_json["displayedRegions"] = [
                {

6:79f7265f90bd

        # We need to know the track type from the config.json generated just before
        track_types = {}
        with open(self.config_json_file, "r") as config_file:
            config_json = json.load(config_file)

        for track_conf in self.tracksToAdd:
            track_types[track_conf["trackId"]] = track_conf["type"]

        for on_track in data["visibility"]["default_on"]:
            style_data = {"type": "LinearBasicDisplay", "height": 100}
            if on_track in data["style"]:

                start = int(loc_match.group(2))
                end = int(loc_match.group(3))
        elif self.genome_name is not None:
            refName = self.genome_name
            start = 0
            end = 100000  # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708

        if refName is not None:
            # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
            view_json["displayedRegions"] = [
                {