# HG changeset patch # User dfornika # Date 1558635397 14400 # Node ID 40ea0695a0a0b2341b17eda76e2b8945266b4bcf # Parent b60b0a9523db91816fc6c3a4f85801f639ea97a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 616f23916e8c71295e1456d6df585c351bd64f86-dirty diff -r b60b0a9523db -r 40ea0695a0a0 data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Fri May 10 20:34:55 2019 -0400 +++ b/data_manager/kraken2_build_database.py Thu May 23 14:16:37 2019 -0400 @@ -140,7 +140,6 @@ member.name = os.path.basename(member.name) fh.extract(member, os.path.join(target_directory, database_path)) - data_table_entry = { 'data_tables': { data_table_name: [ @@ -224,9 +223,12 @@ args = [ '--threads', str(kraken2_args["threads"]), '--download-taxonomy', - '--db', custom_database_name + '--db', custom_database_name, ] + if kraken2_args['skip_maps']: + args += '--skip-maps' + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) args = [ @@ -283,6 +285,7 @@ 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)') + parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='') args = parser.parse_args() data_manager_input = json.loads(open(args.data_manager_json).read()) @@ -330,6 +333,7 @@ elif str(args.database_type) == 'custom': kraken2_args = { "custom_fasta": args.custom_fasta, + "skip_maps": args.skip_maps, "kmer_len": args.kmer_len, "minimizer_len": args.minimizer_len, "minimizer_spaces": args.minimizer_spaces, diff -r b60b0a9523db -r 40ea0695a0a0 data_manager/kraken2_build_database.xml --- a/data_manager/kraken2_build_database.xml Fri May 10 20:34:55 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Thu May 23 14:16:37 2019 -0400 @@ -32,6 +32,7 @@ --minimizer-spaces ${database_type.minimizer_spaces} #else if $database_type.database_type == "custom" --threads \${GALAXY_SLOTS:-1} + ${database_type.skip_maps} --custom-fasta ${database_type.custom_fasta} --custom-database-name ${database_type.custom_database_name} --kmer-len ${database_type.kmer_len} @@ -68,6 +69,7 @@ + diff -r b60b0a9523db -r 40ea0695a0a0 test-data/adapter.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/adapter.fa Thu May 23 14:16:37 2019 -0400 @@ -0,0 +1,2 @@ +>sequence16|kraken:taxid|32630 Adapter sequence +CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA diff -r b60b0a9523db -r 40ea0695a0a0 test-data/adapter.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/adapter.fastq Thu May 23 14:16:37 2019 -0400 @@ -0,0 +1,4 @@ +@sequence16 +CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/hash.k2d Binary file test-data/database/hash.k2d has changed diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/opts.k2d Binary file test-data/database/opts.k2d has changed diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/taxo.k2d Binary file test-data/database/taxo.k2d has changed