| Previous changeset 83:7df5633eacd6 (2021-11-05) Next changeset 85:7316cb684753 (2021-11-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bded7bac774cdcf890076c055f72a48710ce638b-dirty" |
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modified:
data_manager/kraken2_build_database.py |
| b |
| diff -r 7df5633eacd6 -r 0132e84d8572 data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Fri Nov 05 22:30:45 2021 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 05 22:37:45 2021 +0000 |
| b |
| @@ -60,14 +60,6 @@ return self.value -class PrebuiltDates(Enum): - date_2021_05_17 = '2021-05-17' - date_2020_12_02 = '2020-12-02' - - def __str__(self): - return self.value - - 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") @@ -368,7 +360,7 @@ 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=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('--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)') |