| Previous changeset 54:b60b0a9523db (2019-05-10) Next changeset 56:7d384656966e (2019-05-23) |
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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 616f23916e8c71295e1456d6df585c351bd64f86-dirty |
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modified:
data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml |
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added:
test-data/adapter.fa test-data/adapter.fastq test-data/database/hash.k2d test-data/database/opts.k2d test-data/database/taxo.k2d |
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| 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 |
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| @@ -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, |
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| 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 |
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| @@ -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 @@ <when value="custom"> <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" /> + <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> <expand macro="common_params" /> </when> |
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| 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 |
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| @@ -0,0 +1,2 @@ +>sequence16|kraken:taxid|32630 Adapter sequence +CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA |
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| 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 |
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| @@ -0,0 +1,4 @@ +@sequence16 +CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
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| diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/hash.k2d |
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| Binary file test-data/database/hash.k2d has changed |
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| diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/opts.k2d |
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| Binary file test-data/database/opts.k2d has changed |
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| diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/taxo.k2d |
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| Binary file test-data/database/taxo.k2d has changed |