| Previous changeset 50:df30afab73fa (2019-05-03) Next changeset 52:86bc169b0aeb (2019-05-08) |
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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 0dd338db82eaa89c790de452b6da4f63e4081b63-dirty |
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modified:
data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
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| diff -r df30afab73fa -r 2fd3ebc4fcf3 data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Fri May 03 18:52:15 2019 -0400 +++ b/data_manager/kraken2_build_database.py Fri May 03 19:38:34 2019 -0400 |
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| @@ -195,6 +195,52 @@ _add_data_table_entry(data_manager_dict, data_table_entry) +def kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME): + + args = [ + '--threads', str(kraken2_args["threads"]), + '--download-taxonomy', + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--add-to-library', kraken2_args["custom_fasta"], + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--build', + '--kmer-len', str(kraken2_args["kmer_len"]), + '--minimizer-len', str(kraken2_args["minimizer_len"]), + '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, target_directory) + + data_table_entry = { + "value": custom_database_name, + "name": custom_database_name, + "path": custom_database_name + } + + _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) + + def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME): data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] ) @@ -210,8 +256,10 @@ parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces') parser.add_argument('--threads', dest='threads', default=1, help='threads') 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' ) + 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('--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)' ) args = parser.parse_args() data_manager_input = json.loads(open(args.data_manager_json).read()) @@ -260,6 +308,20 @@ kraken2_args, target_directory, ) + elif str(args.database_type) == 'custom': + kraken2_args = { + "custom_fasta": args.custom_fasta, + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + kraken2_build_custom( + data_manager_output, + kraken2_args, + args.custom_database_name, + target_directory, + ) else: sys.exit("Invalid database type") |
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| diff -r df30afab73fa -r 2fd3ebc4fcf3 data_manager/kraken2_build_database.xml --- a/data_manager/kraken2_build_database.xml Fri May 03 18:52:15 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Fri May 03 19:38:34 2019 -0400 |
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| @@ -30,6 +30,13 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + #else if $database_type.database_type == "custom" + --threads \${GALAXY_SLOTS:-1} + --custom-fasta ${database_type.custom_fasta} + --custom-database-name ${database_type.custom_database_name} + --kmer-len ${database_type.kmer_len} + --minimizer-len ${database_type.minimizer_len} + --minimizer-spaces ${database_type.minimizer_spaces} #end if ]]> </command> @@ -59,8 +66,8 @@ <expand macro="common_params" /> </when> <when value="custom"> - <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> - <param name="database_name" type="text" label="Name for this database" /> + <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> + <param name="custom_database_name" type="text" label="Name for this database" /> <expand macro="common_params" /> </when> |