comparison data_manager/kraken2_build_database.py @ 4:0eebe086fd58 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"

3:19b6a2f0dbe2

        now,
        "standard",
        "kmer-len", str(kraken2_args["kmer_len"]),
        "minimizer-len", str(kraken2_args["minimizer_len"]),
        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
    ])

    database_name = " ".join([
        "Standard",
        "(Created:",
        now + ",",
        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
    ])

    database_path = database_value

    args = [
        '--threads', str(kraken2_args["threads"]),
        '--standard',
        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
        '--db', database_path
    ]

    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)

        now,
        kraken2_args["special_database_type"],
        "kmer-len", str(kraken2_args["kmer_len"]),
        "minimizer-len", str(kraken2_args["minimizer_len"]),
        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
    ])

    database_name = " ".join([
        special_database_names[kraken2_args["special_database_type"]],
        "(Created:",
        now + ",",
        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
    ])

    database_path = database_value

    args = [
        '--threads', str(kraken2_args["threads"]),
        '--special', kraken2_args["special_database_type"],
        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
        '--db', database_path
    ]

    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)

        '--threads', str(kraken2_args["threads"]),
        '--build',
        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
        '--db', custom_database_name
    ]

    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)

    parser = argparse.ArgumentParser()
    parser.add_argument('data_manager_json')
    parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
    parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
    parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
    parser.add_argument('--threads', dest='threads', default=1, help='threads')
    parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
    parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
    parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
    parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')

    if str(args.database_type) == 'standard':
        kraken2_args = {
            "kmer_len": args.kmer_len,
            "minimizer_len": args.minimizer_len,
            "minimizer_spaces": args.minimizer_spaces,
            "threads": args.threads,
            "clean": args.clean,
        }
        data_manager_output = kraken2_build_standard(
            kraken2_args,

        kraken2_args = {
            "special_database_type": str(args.special_database_type),
            "kmer_len": args.kmer_len,
            "minimizer_len": args.minimizer_len,
            "minimizer_spaces": args.minimizer_spaces,
            "threads": args.threads,
            "clean": args.clean,
        }
        data_manager_output = kraken2_build_special(
            kraken2_args,

            "custom_fasta": args.custom_fasta,
            "skip_maps": args.skip_maps,
            "kmer_len": args.kmer_len,
            "minimizer_len": args.minimizer_len,
            "minimizer_spaces": args.minimizer_spaces,
            "threads": args.threads,
            "clean": args.clean,
        }
        data_manager_output = kraken2_build_custom(
            kraken2_args,

4:0eebe086fd58

        now,
        "standard",
        "kmer-len", str(kraken2_args["kmer_len"]),
        "minimizer-len", str(kraken2_args["minimizer_len"]),
        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
        "load-factor", str(kraken2_args["load_factor"]),
    ])

    database_name = " ".join([
        "Standard",
        "(Created:",
        now + ",",
        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
        "load-factor", str(kraken2_args["load_factor"]),
    ])

    database_path = database_value

    args = [
        '--threads', str(kraken2_args["threads"]),
        '--standard',
        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
        '--load-factor', str(kraken2_args["load_factor"]),
        '--db', database_path
    ]

    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)

        now,
        kraken2_args["special_database_type"],
        "kmer-len", str(kraken2_args["kmer_len"]),
        "minimizer-len", str(kraken2_args["minimizer_len"]),
        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
        "load-factor", str(kraken2_args["load_factor"]),
    ])

    database_name = " ".join([
        special_database_names[kraken2_args["special_database_type"]],
        "(Created:",
        now + ",",
        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
        "load-factor=" + str(kraken2_args["load_factor"]) + ")",
    ])

    database_path = database_value

    args = [
        '--threads', str(kraken2_args["threads"]),
        '--special', kraken2_args["special_database_type"],
        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
        '--load-factor', str(kraken2_args["load_factor"]),
        '--db', database_path
    ]

    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)

        '--threads', str(kraken2_args["threads"]),
        '--build',
        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
        '--load-factor', str(kraken2_args["load_factor"]),
        '--db', custom_database_name
    ]

    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)

    parser = argparse.ArgumentParser()
    parser.add_argument('data_manager_json')
    parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
    parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
    parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
    parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
    parser.add_argument('--threads', dest='threads', default=1, help='threads')
    parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
    parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
    parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
    parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')

    if str(args.database_type) == 'standard':
        kraken2_args = {
            "kmer_len": args.kmer_len,
            "minimizer_len": args.minimizer_len,
            "minimizer_spaces": args.minimizer_spaces,
            "load_factor": args.load_factor,
            "threads": args.threads,
            "clean": args.clean,
        }
        data_manager_output = kraken2_build_standard(
            kraken2_args,

        kraken2_args = {
            "special_database_type": str(args.special_database_type),
            "kmer_len": args.kmer_len,
            "minimizer_len": args.minimizer_len,
            "minimizer_spaces": args.minimizer_spaces,
            "load_factor": args.load_factor,
            "threads": args.threads,
            "clean": args.clean,
        }
        data_manager_output = kraken2_build_special(
            kraken2_args,

            "custom_fasta": args.custom_fasta,
            "skip_maps": args.skip_maps,
            "kmer_len": args.kmer_len,
            "minimizer_len": args.minimizer_len,
            "minimizer_spaces": args.minimizer_spaces,
            "load_factor": args.load_factor,
            "threads": args.threads,
            "clean": args.clean,
        }
        data_manager_output = kraken2_build_custom(
            kraken2_args,