Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 70:93b67ce30fcf 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 19:06:16 +0000 |
| parents | 37467f9b7ea3 |
| children | 8bcfc243de44 |
| files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
| diffstat | 2 files changed, 2 insertions(+), 1 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Fri Nov 05 18:55:37 2021 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 05 19:06:16 2021 +0000 @@ -367,7 +367,7 @@ 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', 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('--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)')
--- a/data_manager/kraken2_build_database.xml Fri Nov 05 18:55:37 2021 +0000 +++ b/data_manager/kraken2_build_database.xml Fri Nov 05 19:06:16 2021 +0000 @@ -25,6 +25,7 @@ --minikraken2-version ${database_type.minikraken2_version} #else if $database_type.database_type == "standard_prebuilt" --standard-prebuilt-size ${database_type.standard_prebuilt_size} + --prebuilt-date ${database_type.prebuilt_date} #else if $database_type.database_type == "standard_local_build" --threads \${GALAXY_SLOTS:-1} --kmer-len ${database_type.kmer_len}