Mercurial > repos > dfornika > data_manager_build_bracken_database
changeset 20:4ee8002597d2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3-dirty"
| author | dfornika |
|---|---|
| date | Thu, 04 Nov 2021 22:52:51 +0000 |
| parents | 9c4f30740a71 |
| children | 09825e7c8b05 |
| files | data_manager/bracken_build_database.py data_manager/bracken_build_database.xml |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager/bracken_build_database.py Thu Nov 04 22:49:26 2021 +0000 +++ b/data_manager/bracken_build_database.py Thu Nov 04 22:52:51 2021 +0000 @@ -54,7 +54,7 @@ parser.add_argument('--read-len', dest='read_len', help='Read length') parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database') parser.add_argument('--database-name', dest='database_name', help='Database Name') - parser.add_argument('--prebuilt', dest='prebuilt', help='Use pre-built DB') + parser.add_argument('--prebuilt', action='store_true', dest='prebuilt', help='Use pre-built DB') args = parser.parse_args() with open(args.data_manager_json) as fh:
--- a/data_manager/bracken_build_database.xml Thu Nov 04 22:49:26 2021 +0000 +++ b/data_manager/bracken_build_database.xml Thu Nov 04 22:52:51 2021 +0000 @@ -11,7 +11,7 @@ #set db_dir = os.path.basename($kraken_db.fields.path) mkdir '$db_dir' && - ln -s '${kraken_db.fields.path}'/* '$db_dir/' && + ln -s '${kraken_db.fields.path}/*' '$db_dir/' && python '$__tool_directory__/bracken_build_database.py' '${out_file}' --kraken-db '$db_dir'