Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 72:b1db190792e2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit cec255ceca4b1dd39c4b5795cbfcf5f8e74fc9c7-dirty"
| author | dfornika |
|---|---|
| date | Fri, 05 Nov 2021 19:19:50 +0000 |
| parents | 8bcfc243de44 |
| children | 7bda019d3d0c |
| files | data_manager/kraken2_build_database.py |
| diffstat | 1 files changed, 10 insertions(+), 8 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Fri Nov 05 19:08:15 2021 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 05 19:19:50 2021 +0000 @@ -51,13 +51,6 @@ return self.value -class PrebuiltDate(Enum): - date_20210517 = '2021-05-17' - date_20201202 = '2020-12-02' - - def __str__(self): - return self.value - class StandardPrebuiltSizes(Enum): full = 'full' gb_16 = '16' @@ -67,6 +60,15 @@ return self.value +class PrebuiltDates(): + dates = [ + '2021-05-17', + '2020-12-02', + ] + + def __str__(self): + return str(self.dates) + def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") @@ -367,7 +369,7 @@ 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('--standard-prebuilt-size', dest='standard_prebuilt_size', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Size of standard prebuilt database to download (only applies to --database-type standard_prebuilt. Options are: "8", "16", "full".)') - parser.add_argument('--prebuilt-date', dest='prebuilt_date', type=PrebuiltDate, choices=list(PrebuiltDate), help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt. Options are: "2021-05-17", "2020-12-02".)') + parser.add_argument('--prebuilt-date', dest='prebuilt_date', type=PrebuiltDates, choices=list(PrebuiltDates), help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt. Options are: "2021-05-17", "2020-12-02".)') 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)')