comparison data_manager/install_primer_scheme_bedfiles.py @ 4:157a5c9ea72a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

3:a2953ef09fe1

        print(
            "Only one of --artic_primers or --primer_file + --primer_name + --primer_description can be chosen"
        )
        exit(1)

    config = json.load(open(args.galaxy_datamanager_filename))
    output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
    if output_directory is None:
        output_directory = args.output_directory

    if not os.path.isdir(output_directory):
        os.makedirs(output_directory)

    data_manager_dict = {}
    data_manager_dict["data_tables"] = json.load(
        open(args.galaxy_datamanager_filename)
    ).get("data_tables", {})
    data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {})
    data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[
        "data_tables"
    ].get(DATA_TABLE_NAME, [])

    if args.artic_primers:

            args.primer_name,
            args.primer_description,
        )

    data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data)
    print(data_manager_dict)
    json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w"))

4:157a5c9ea72a

        print(
            "Only one of --artic_primers or --primer_file + --primer_name + --primer_description can be chosen"
        )
        exit(1)

    with open(args.galaxy_datamanager_filename) as fh:
        config = json.load(fh)
    output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
    if output_directory is None:
        output_directory = args.output_directory

    if not os.path.isdir(output_directory):
        os.makedirs(output_directory)

    data_manager_dict = {}
    data_manager_dict["data_tables"] = config.get("data_tables", {})
    data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[
        "data_tables"
    ].get(DATA_TABLE_NAME, [])

    if args.artic_primers:

            args.primer_name,
            args.primer_description,
        )

    data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data)
    with open(args.galaxy_datamanager_filename, "w") as fh:
        json.dump(data_manager_dict, fh, sort_keys=True)