Mercurial > repos > iuc > data_manager_build_bracken_database
changeset 3:3c7d2c84cb09 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
| author | iuc |
|---|---|
| date | Mon, 08 Nov 2021 15:51:51 +0000 |
| parents | fd5830f88314 |
| children | c8136920948b |
| files | data_manager/bracken_build_database.py data_manager/bracken_build_database.xml data_manager_conf.xml |
| diffstat | 3 files changed, 60 insertions(+), 24 deletions(-) [+] |
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--- a/data_manager/bracken_build_database.py Sun Nov 22 12:45:23 2020 +0000 +++ b/data_manager/bracken_build_database.py Mon Nov 08 15:51:51 2021 +0000 @@ -13,7 +13,7 @@ DATA_TABLE_NAME = "bracken_databases" -def bracken_build_database(target_directory, bracken_build_args, database_name, data_table_name=DATA_TABLE_NAME): +def bracken_build_database(target_directory, bracken_build_args, database_name, prebuilt=False, data_table_name=DATA_TABLE_NAME): database_value = str(uuid.uuid4()) @@ -21,14 +21,15 @@ database_path = os.path.join(bracken_build_args['kraken_database'], 'database' + str(bracken_build_args['read_len']) + 'mers.kmer_distrib') - bracken_build_args_list = [ - '-t', bracken_build_args['threads'], - '-k', bracken_build_args['kmer_len'], - '-l', bracken_build_args['read_len'], - '-d', bracken_build_args['kraken_database'], - ] + if not prebuilt: + bracken_build_args_list = [ + '-t', bracken_build_args['threads'], + '-k', bracken_build_args['kmer_len'], + '-l', bracken_build_args['read_len'], + '-d', bracken_build_args['kraken_database'], + ] - subprocess.check_call(['bracken-build'] + bracken_build_args_list) + subprocess.check_call(['bracken-build'] + bracken_build_args_list) data_table_entry = { "data_tables": { @@ -53,6 +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', action='store_true', dest='prebuilt', help='Use pre-built DB') args = parser.parse_args() with open(args.data_manager_json) as fh: @@ -60,12 +62,19 @@ target_directory = data_manager_input['output_data'][0]['extra_files_path'] - bracken_build_args = { - 'threads': args.threads, - 'kmer_len': args.kmer_len, - 'read_len': args.read_len, - 'kraken_database': args.kraken_database, - } + if args.prebuilt: + bracken_build_args = { + 'threads': args.threads, + 'read_len': args.read_len, + 'kraken_database': args.kraken_database, + } + else: + bracken_build_args = { + 'threads': args.threads, + 'kmer_len': args.kmer_len, + 'read_len': args.read_len, + 'kraken_database': args.kraken_database, + } try: os.mkdir(target_directory) @@ -81,6 +90,7 @@ target_directory, bracken_build_args, args.database_name, + args.prebuilt, ) with open(args.data_manager_json, 'w') as fh:
--- a/data_manager/bracken_build_database.xml Sun Nov 22 12:45:23 2020 +0000 +++ b/data_manager/bracken_build_database.xml Mon Nov 08 15:51:51 2021 +0000 @@ -1,9 +1,9 @@ <?xml version="1.0"?> -<tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy0" profile="19.01"> +<tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy1" profile="19.01"> <description>bracken database builder</description> <requirements> <requirement type="package" version="2.5">bracken</requirement> - <requirement type="package" version="2.0.8_beta">kraken2</requirement> + <requirement type="package" version="2.1.1">kraken2</requirement> </requirements> <command> <![CDATA[ @@ -11,13 +11,20 @@ #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' + --threads \${GALAXY_SLOTS:-1} - --kmer-len ${kmer_len} - --read-len ${read_len} + #if $check_prebuilt.prebuilt == "no" + --kraken-db '$db_dir' + --kmer-len ${check_prebuilt.kmer_len} + #end if + #if $check_prebuilt.prebuilt == "yes" + --kraken-db '${kraken_db.fields.path}' + --prebuilt + #end if + --read-len ${check_prebuilt.read_len} --database-name '${database_name}' ]]> </command> @@ -27,9 +34,28 @@ <validator type="no_options" message="No Kraken2 databases are available" /> </options> </param> - <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> - <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> - <param name="database_name" type="text" label="Database Name" /> + <conditional name="check_prebuilt"> + <param name="prebuilt" type="select" label="Use Pre-built DB"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> + <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> + </when> + <when value="yes"> + <param name="read_len" type="select" label="Read length" > + <option value="50">50</option> + <option value="75">75</option> + <option value="100">100</option> + <option value="150">150</option> + <option value="200">200</option> + <option value="250">250</option> + <option value="300">300</option> + </param> + </when> + </conditional> + <param name="database_name" type="text" label="Database Name" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" />
--- a/data_manager_conf.xml Sun Nov 22 12:45:23 2020 +0000 +++ b/data_manager_conf.xml Mon Nov 08 15:51:51 2021 +0000 @@ -1,5 +1,5 @@ <data_managers> - <data_manager tool_file="data_manager/bracken_build_database.xml" id="bracken_build_database" version="2.5+galaxy0"> + <data_manager tool_file="data_manager/bracken_build_database.xml" id="bracken_build_database" version="2.6+galaxy0"> <data_table name="bracken_databases"> <output> <column name="value"/>