comparison data_manager/kraken2_build_database.py @ 13:e9ee4d074d5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a

12:90b4d4f0a3a4

class KrakenDatabaseTypes(Enum):
    standard_local_build = 'standard_local_build'
    standard_prebuilt = 'standard_prebuilt'
    minikraken = 'minikraken'
    special = 'special'
    custom = 'custom'

    def __str__(self):
        return self.value

    pluspf_08gb = "pluspf_08gb"
    pluspf_16gb = "pluspf_16gb"
    pluspfp = "pluspfp"
    pluspfp_08gb = "pluspfp_08gb"
    pluspfp_16gb = "pluspfp_16gb"

    def __str__(self):
        return self.value

        'pluspf': "PlusPF (Standard plus protozoa and fungi)",
        'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
        'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
        'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
        'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
        'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)"
    }

    database_value = "_".join([
        now,
        "standard_prebuilt",

    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('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt.')
    parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
    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)')
    parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
    parser.add_argument('--custom-source-info', dest='custom_source_info', help='Description of how this build has been sourced (only applies to --database-type custom)')

        }
        data_manager_output = kraken2_build_standard(
            kraken2_args,
            target_directory,
        )
    elif str(args.database_type) == 'standard_prebuilt':
        data_manager_output = kraken2_build_standard_prebuilt(
            str(args.prebuilt_db),
            str(args.prebuilt_date),
            target_directory
        )

13:e9ee4d074d5d

class KrakenDatabaseTypes(Enum):
    standard_local_build = 'standard_local_build'
    standard_prebuilt = 'standard_prebuilt'
    minikraken = 'minikraken'
    special_prebuilt = 'special_prebuilt'
    special = 'special'
    custom = 'custom'

    def __str__(self):
        return self.value

    pluspf_08gb = "pluspf_08gb"
    pluspf_16gb = "pluspf_16gb"
    pluspfp = "pluspfp"
    pluspfp_08gb = "pluspfp_08gb"
    pluspfp_16gb = "pluspfp_16gb"
    eupathdb48 = "eupathdb48"

    def __str__(self):
        return self.value

        'pluspf': "PlusPF (Standard plus protozoa and fungi)",
        'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
        'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
        'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
        'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
        'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)",
        'eupathdb48': "EuPathDB-46",
    }

    database_value = "_".join([
        now,
        "standard_prebuilt",

    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('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt or special_prebuilt.')
    parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
    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)')
    parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
    parser.add_argument('--custom-source-info', dest='custom_source_info', help='Description of how this build has been sourced (only applies to --database-type custom)')

        }
        data_manager_output = kraken2_build_standard(
            kraken2_args,
            target_directory,
        )
    elif str(args.database_type) in ('standard_prebuilt', 'special_prebuilt'):
        data_manager_output = kraken2_build_standard_prebuilt(
            str(args.prebuilt_db),
            str(args.prebuilt_date),
            target_directory
        )