| Previous changeset 72:b1db190792e2 (2021-11-05) Next changeset 74:d7a452cd17fb (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 cec255ceca4b1dd39c4b5795cbfcf5f8e74fc9c7-dirty" |
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modified:
data_manager/kraken2_build_database.py |
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added:
test.json |
| b |
| diff -r b1db190792e2 -r 7bda019d3d0c data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Fri Nov 05 19:19:50 2021 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 05 19:34:04 2021 +0000 |
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| @@ -60,14 +60,14 @@ return self.value -class PrebuiltDates(): - dates = [ - '2021-05-17', - '2020-12-02', - ] +class PrebuiltDates(Enum): + date_2021_05_17 = '2021-05-17' + date_2020_12_02 = '2020-12-02' def __str__(self): - return str(self.dates) + 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") |
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| diff -r b1db190792e2 -r 7bda019d3d0c test.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.json Fri Nov 05 19:34:04 2021 +0000 |
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| @@ -0,0 +1,50 @@ +{ + "param_dict": { + "chromInfo": "/galaxy-central/tool-data/shared/ucsc/chrom/?.len", + "input": "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX", + "__datatypes_config__": "/export/galaxy-central/database/job_working_directory/000/24/registry.xml", + "GALAXY_DATATYPES_CONF_FILE": "/export/galaxy-central/database/job_working_directory/000/24/registry.xml", + "__history_id__": "f597429621d6eb2b", + "__galaxy_url__": "http://localhost", + "database_type": { + "database_type": "standard_prebuilt", + "__current_case__": "1", + "standard_prebuilt_size": "8", + "prebuilt_date": "2021-05-27" + }, + "dbkey": "?", + "__input_ext": "input", + "__user__": "galaxy.model:SafeStringWrapper(galaxy.model.User:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'galaxy.util.object_wrapper.SafeStringWrapper'>,<class 'numbers.Number'>)", + "__user_id__": "1", + "userId": "1", + "__user_email__": "admin@galaxy.org", + "userEmail": "admin@galaxy.org", + "__user_name__": "admin", + "out_file": "/export/galaxy-central/database/files/000/dataset_26.dat", + "__tool_directory__": "/galaxy-central/database/shed_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data_manager_build_kraken2_database/80e778af6c6c/data_manager_build_kraken2_database/data_manager", + "__get_data_table_entry__": "<function ToolEvaluator.__populate_non_job_params.<locals>.get_data_table_entry at 0x7f1950018048>", + "__local_working_directory__": "/export/galaxy-central/database/job_working_directory/000/24", + "__app__": "galaxy.app:UniverseApplication", + "__new_file_path__": "/export/galaxy-central/database/files", + "__tool_data_path__": "/galaxy-central/tool-data", + "GALAXY_DATA_INDEX_DIR": "/galaxy-central/tool-data", + "__root_dir__": "/galaxy-central", + "GALAXY_ROOT_DIR": "/galaxy-central", + "__admin_users__": "admin@galaxy.org" + }, + "output_data": [ + { + "out_data_name": "out_file", + "ext": "data_manager_json", + "dataset_id": 26, + "hda_id": 28, + "file_name": "/export/galaxy-central/database/files/000/dataset_26.dat", + "extra_files_path": "/export/galaxy-central/database/job_working_directory/000/24/working/dataset_26_files" + } + ], + "job_config": { + "GALAXY_DATATYPES_CONF_FILE": "/export/galaxy-central/database/job_working_directory/000/24/registry.xml", + "GALAXY_ROOT_DIR": "/galaxy-central", + "TOOL_PROVIDED_JOB_METADATA_FILE": "galaxy.json" + } +} |