| Previous changeset 7:678176bff643 (2024-05-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db |
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modified:
data_manager/dada2_fetcher.xml test-data/PR24.11.1_json test-data/RefSeq_RDP2018_json test-data/dada2_species.loc test-data/dada2_taxonomy.loc test-data/greengenes13.84_json test-data/gtdb2018_json test-data/hitdb1_json test-data/rdp16_json test-data/silva132_json test-data/silva138_json test-data/silvaeuk132_json test-data/unite8fungi_json test-data/unite8fungisingletons_json |
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removed:
data_manager/data_manager.py |
| b |
| diff -r 678176bff643 -r 0181efacb40a data_manager/dada2_fetcher.xml --- a/data_manager/dada2_fetcher.xml Tue May 21 07:35:56 2024 +0000 +++ b/data_manager/dada2_fetcher.xml Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| b'@@ -1,139 +1,361 @@\n-<?xml version="1.0"?>\n-<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.1" profile="23.0">\n+<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.2" profile="24.2">\n <description>Download reference databases</description>\n <requirements>\n- <requirement type="package" version="3.7">python</requirement>\n+ <requirement type="package" version="1.25.0">wget</requirement>\n+ <requirement type="package" version="6.0">unzip</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n- python \'$__tool_directory__/data_manager.py\'\n- --out \'$out_file\'\n- #set dataset = str($db_cond.db_select) + \'_\' + str($db_cond.version_select)\n- --dataset \'$dataset\'\n+## see https://github.com/benjjneb/dada2/issues/2053 for the distinction of the _toGenus and _toSpecies datasets\n+#set $FILE2TAXURL = {\n+ "silva_138.2_toGenus": "https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toGenus_trainset.fa.gz?download=1",\n+ "silva_138.2_toSpecies": "https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toSpecies_trainset.fa.gz?download=1",\n+\n+ "silva_138.2_fungi_18S_toGenus": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_nr99_v138_2_toGenus_trainset.fasta?download=1",\n+ "silva_138.2_fungi_18S_toSpecies": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_nr99_v138_2_toSpecies_trainset.fasta?download=1",\n+\n+ "silva_138.2_fungi_26S_toGenus": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_nr99_v138_2_toGenus_trainset.fasta?download=1",\n+ "silva_138.2_fungi_26S_toSpecies": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_nr99_v138_2_toSpecies_trainset.fasta?download=1",\n+\n+ "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1",\n+ "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1",\n+ "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",\n+ "rdp_19_toGenus": "https://zenodo.org/records/14168771/files/rdp_19_toGenus_trainset.fa.gz?download=1",\n+ "rdp_19_toSpecies": "https://zenodo.org/records/14168771/files/rdp_19_toSpecies_trainset.fa.gz?download=1",\n+ "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",\n+ "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",\n+ "unite_8.0_fungi": "https://s3.hpc.ut.ee/plutof-public/original/9f7b41c3-825b-4db8-9c52-74a4603a860a.zip",\n+ "unite_8.0_fungi_singletons": "https://s3.hpc.ut.ee/plutof-public/original/53dfc9ce-9cb5-4205-84bb-f47faff26462.zip",\n+ "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",\n+ "greengenes2_2024.09_toGenus": "https://zenodo.org/records/14169078/files/gg2_2024_09_toGenus_trainset.fa.gz?download=1",\n+ "greengenes2_2024.09_toSpecies": "https://zenodo.org/records/14169078/files/gg2_2024_09_toSpecies_trainset.fa.gz?download=1",\n+ "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1",\n+\n+ "gtdb_202_toGenus": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_Genus.fa.gz?download=1",\n+ "gtdb_202_toSpecies": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_Species.fa.gz?download=1",\n+ "gtdb_2018_11": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1",\n+\n+ "hitdb_1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1",\n+ "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1",\n+ "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz"\n+}\n+## rdp_19 not available for assignSpecies https://github.com/benjjneb/dada2/issues/2053#issuecomment-2512185929'..b' value="2018_11"/>\n+ <param name="taxonomy_databases" value="RefSeq_RDP_2018_05"/>\n+ <output name="out_file" file="RefSeq_RDP2018_json"/>\n+ <assert_command>\n+ <has_text text="wget" n="1"/>\n+ </assert_command>\n+ </test>\n+\n+ <test>\n+ <param name="taxonomy_databases" value="gtdb_202_toGenus,gtdb_202_toSpecies"/>\n+ <param name="species_databases" value="gtdb_202"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text=""GTDB Version 202 to Genus (for short reads)""/>\n+ <has_text text=""GTDB Version 202 to Species (for long reads)""/>\n+ <has_text text=""GTDB Version 202""/>\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <has_text text="wget" n="3"/>\n+ </assert_command>\n+ </test>\n+\n+ <test>\n+ <param name="taxonomy_databases" value="gtdb_2018_11"/>\n+ <param name="species_databases" value="gtdb_2018_11"/>\n <output name="out_file" file="gtdb2018_json"/>\n+ <assert_command>\n+ <has_text text="wget" n="2"/>\n+ </assert_command>\n </test>\n <test>\n- <param name="db_cond|db_select" value="hitdb"/>\n- <param name="db_cond|version_select" value="1"/>\n+ <param name="taxonomy_databases" value="hitdb_1"/>\n <output name="out_file" file="hitdb1_json"/>\n+ <assert_command>\n+ <has_text text="wget" n="1"/>\n+ </assert_command>\n </test>\n <test>\n- <param name="db_cond|db_select" value="silva_euk_18S"/>\n- <param name="db_cond|version_select" value="132"/>\n+ <param name="taxonomy_databases" value="silva_euk_18S_132"/>\n <output name="out_file" file="silvaeuk132_json"/>\n+ <assert_command>\n+ <has_text text="wget" n="1"/>\n+ </assert_command>\n </test>\n <test>\n- <param name="db_cond|db_select" value="PR2"/>\n- <param name="db_cond|version_select" value="4.11.1"/>\n+ <param name="taxonomy_databases" value="PR2_4.11.1"/>\n <output name="out_file" file="PR24.11.1_json"/>\n+ <assert_command>\n+ <has_text text="wget" n="1"/>\n+ </assert_command>\n </test>\n </tests>\n <help><![CDATA[\n@@ -142,14 +364,15 @@\n \n The following refrence databases which are describes as maintained by the DADA2 project (https://benjjneb.github.io/dada2/training.html) are available\n \n-- Silva (https://www.arb-silva.de/)\n+- Silva\n - RDP\n-- GreenGenes (http://greengenes.secondgenome.com/)\n+- GreenGenes (https://web.archive.org/web/20240703054246/https://greengenes.secondgenome.com/)\n+- Greengenes2 (https://greengenes2.ucsd.edu/)\n - UNITE general FASTA (https://unite.ut.ee/repository.php)\n \n While Silva and RDP contain reference databases for taxonomy and species assignment, the greengenes and UNITE databases only contains a reference database for taxonomy assignment.\n \n-For the Silva databases check the license information: http://www.arb-silva.de/silva-license-information.\n+Silva are licensed under Create Commons Attribution 4.0 (CC-BY 4.0) since release 138.\n \n Except for UNITE all reference databases are downloaded from the corresponding zenodo links that are listed on the DADA2 website. The UNITE databases are taken from the links provided on the UNITE website\n \n@@ -176,6 +399,8 @@\n <citation type="doi">10.1093/nar/gks1219</citation>\n <!-- rdp -->\n <citation type="doi">10.1093/nar/gkt1244</citation>\n+ <!-- greengenes2 -->\n+ <citation type="doi">10.1038/s41587-023-01845-1</citation>\n <!-- greengenes -->\n <citation type="doi">10.1128/AEM.03006-05</citation>\n <!-- unite -->\n' |
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| diff -r 678176bff643 -r 0181efacb40a data_manager/data_manager.py --- a/data_manager/data_manager.py Tue May 21 07:35:56 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,136 +0,0 @@ -import argparse -import json -import os -try: - # For Python 3.0 and later - from urllib.request import Request, urlopen -except ImportError: - # Fall back to Python 2 imports - from urllib2 import Request, urlopen - -DEFAULT_TAXLEVELS = "Kingdom,Phylum,Class,Order,Family,Genus,Species" - -FILE2NAME = { - "silva_138": "Silva version 138", - "silva_132": "Silva version 132", - "silva_128": "Silva version 128", - "rdp_16": "RDP trainset 16", - "rdp_14": "RDP trainset 14", - "greengenes_13.84": "GreenGenes version 13.84", - "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi", - "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", - "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", - "gtdb_2018_11": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", - "hitdb_1": "HitDB version 1 (Human InTestinal 16S rRNA)", - "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S", - "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1" -} - -FILE2TAXURL = { - "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1", - "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1", - "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", - "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", - "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1", - "unite_8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip", - "unite_8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip", - "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1", - "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1", - "gtdb_2018_11": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1", - "hitdb_1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1", - "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1", - "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz" -} - -FILE2SPECIESURL = { - "silva_138": "https://zenodo.org/record/3731176/files/silva_species_assignment_v138.fa.gz?download=1", - "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1", - "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1", - "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1", - "rdp_14": "https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1" -} - -FILE2TAXLEVELS = { - "PR2_4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species" -} - - -def url_download(url, fname, workdir): - """ - download url to workdir/fname - """ - file_path = os.path.join(workdir, fname) - if not os.path.exists(workdir): - os.makedirs(workdir) - src = None - dst = None - try: - req = Request(url) - src = urlopen(req) - with open(file_path, 'wb') as dst: - while True: - chunk = src.read(2**10) - if chunk: - dst.write(chunk) - else: - break - finally: - if src: - src.close() - -# special treatment of UNITE DBs: they are zip files containing two fasta (xyz.fasta and developer/xyz.fasta) - if fname.startswith("unite"): - import glob - import gzip - import shutil - import zipfile - # unzip download - zip_ref = zipfile.ZipFile(file_path, 'r') - zip_ref.extractall(workdir) - zip_ref.close() - # gzip top level fasta file - fastas = glob.glob("%s/*fasta" % workdir) - if len(fastas) != 1: - msg = "UNITE download %s contained %d fasta file(s): %s" % (url, len(fastas), " ".join(fastas)) - raise Exception(msg) - with open(fastas[0], 'rb') as f_in: - with gzip.open(file_path, 'wb') as f_out: - shutil.copyfileobj(f_in, f_out) - - -def remote_dataset(dataset, outjson): - - with open(outjson) as fh: - params = json.load(fh) - - workdir = params['output_data'][0]['extra_files_path'] - os.mkdir(workdir) - url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir) - - data_manager_json = {"data_tables": {}} - data_manager_entry = {} - data_manager_entry['value'] = dataset - data_manager_entry['name'] = FILE2NAME[dataset] - data_manager_entry['path'] = dataset + ".taxonomy" - data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS) - data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry - - if FILE2SPECIESURL.get(dataset, False): - url_download(FILE2SPECIESURL[dataset], dataset + ".species", workdir) - data_manager_entry = {} - data_manager_entry['value'] = dataset - data_manager_entry['name'] = FILE2NAME[dataset] - data_manager_entry['path'] = dataset + ".species" - data_manager_json["data_tables"]["dada2_species"] = data_manager_entry - - with open(outjson, 'w') as fh: - json.dump(data_manager_json, fh, sort_keys=True) - - -if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Create data manager json.') - parser.add_argument('--out', action='store', help='JSON filename') - parser.add_argument('--dataset', action='store', help='Download data set name') - args = parser.parse_args() - - remote_dataset(args.dataset, args.out) |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/PR24.11.1_json --- a/test-data/PR24.11.1_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/PR24.11.1_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "Protist Ribosomal Reference database (PR2) 4.11.1", "path": "PR2_4.11.1.taxonomy", "taxlevels": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species", "value": "PR2_4.11.1"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "PR2_4.11.1", + "name": "Protist Ribosomal Reference database (PR2) 4.11.1", + "path": "PR2_4.11.1.taxonomy", + "taxlevels": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/RefSeq_RDP2018_json --- a/test-data/RefSeq_RDP2018_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/RefSeq_RDP2018_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", "path": "RefSeq_RDP_2018_05.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "RefSeq_RDP_2018_05"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "RefSeq_RDP_2018_05", + "name": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", + "path": "RefSeq_RDP_2018_05.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +} |
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| diff -r 678176bff643 -r 0181efacb40a test-data/dada2_species.loc --- a/test-data/dada2_species.loc Tue May 21 07:35:56 2024 +0000 +++ b/test-data/dada2_species.loc Sat Nov 22 20:07:44 2025 +0000 |
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| @@ -7,3 +7,62 @@ # Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html # # Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html +silva_138 Silva version 138 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.species +silva_138 Silva version 138 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138 Silva version 138 /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/silva_138.taxonomy +silva_132 Silva version 132 /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/silva_132.taxonomy +rdp_16 RDP trainset 16 /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/rdp_16.taxonomy +silva_138 Silva version 138 /tmp/tmp7bm731ex/galaxy-dev/tool-data/dada2/silva_138.taxonomy +silva_138.2 Silva version 138.2 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_138.2.taxonomy +silva_138 Silva version 138 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_138.taxonomy +silva_132 Silva version 132 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_132.taxonomy +rdp_16 RDP trainset 16 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/rdp_16.taxonomy +silva_138 Silva version 138 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138 Silva version 138 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138 Silva version 138 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138.2 Silva version 138.2 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138 Silva version 138 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138.2 Silva version 138.2 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138.2 Silva version 138.2 /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.species +silva_138.2 Silva version 138.2 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/rdp_16.species +gtdb_202 GTDB Version 202 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/gtdb_202.species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/gtdb_2018_11.species +silva_138.2 Silva version 138.2 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/rdp_16.species +gtdb_202 GTDB Version 202 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/gtdb_202.species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/gtdb_2018_11.species +silva_138.2 Silva version 138.2 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_16.species +gtdb_202 GTDB Version 202 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_202.species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_2018_11.species |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/dada2_taxonomy.loc --- a/test-data/dada2_taxonomy.loc Tue May 21 07:35:56 2024 +0000 +++ b/test-data/dada2_taxonomy.loc Sat Nov 22 20:07:44 2025 +0000 |
| b |
| b'@@ -7,3 +7,270 @@\n # Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html\n # \n # taxlevels is a comma separated list of taxonomy levels\n+silva_138.2_toGenus\tSilva version 138.2 to Genus (for short read 16S)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_toSpecies\tSilva version 138.2 to Species (for long read 16S)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138\tSilva version 138\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138\tSilva version 138\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_132\tSilva version 132\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_132.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+rdp_19_toSpecies\tRDP trainset 19 to Species (for long read 16S)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+rdp_19_toGenus\tRDP trainset 19 to Genus (for short read 16S)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+rdp_16\tRDP trainset 16\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_16.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+greengenes2_2024.09_toGenus\tGreenGenes2 release 2024.09 to Genus (for short read 16S)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+greengenes2_2024.09_toSpecies\tGreenGenes2 release 2024.09 to Species (for long read 16S)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+unite_8.0_fungi\tUNITE: General Fasta release 8.0 for Fungi\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+unite_8.0_fungi_singletons\tUNITE: General Fasta release 8.0 for Fungi including global and 97% singletons\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+RefSeq_RDP_2018_05\tNCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+gtdb_2018_11\tGTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+hitdb_1\tHitDB version 1 (Human InTestinal 16S rRNA)\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_euk_18S_132\tSilva version 132 Eukaryotic 18S\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+PR2_4.11.1\tProtist Ribosomal Reference database (PR2) 4.11.1\t/tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy\tKingdom,Supergroup,Division,Class,Order,Family,Genus,Species\n+silva_138.2_toGenus\tSilva version 138.2 to Genus (for short read 16S)\t/tmp/tmpbccvw1gs/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_toSpecies\tSilva version 138.2 to Species (for long read 16S)\t/tmp/tmpbccvw1gs/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_toGenus\tSilva version 138.2 to Genus (for short read 16S)\t/tmp/tmpexepu7wk/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_toSpecies\tSilva version 138.2 to Species (for long read 16S)\t/tmp/tmpexepu7wk/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Spe'..b'my\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_fungi_18S_toGenus\tSilva version 138.2 for Fungi 18S to Genus (for short reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_fungi_18S_toSpecies\tSilva version 138.2 for Fungi 18S to Species (for long reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_fungi_26S_toGenus\tSilva version 138.2 for Fungi 26S to Genus (for short reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138.2_fungi_26S_toSpecies\tSilva version 138.2 for Fungi 26S to Species (for long reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_138\tSilva version 138\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_132\tSilva version 132\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_132.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+rdp_19_toSpecies\tRDP trainset 19 to Species (for long reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+rdp_19_toGenus\tRDP trainset 19 to Genus (for short reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+rdp_16\tRDP trainset 16\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_16.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+greengenes2_2024.09_toSpecies\tGreenGenes2 release 2024.09 to Species (for long reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+greengenes2_2024.09_toGenus\tGreenGenes2 release 2024.09 to Genus (for short reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+greengenes_13.84\tGreenGenes version 13.84\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+unite_8.0_fungi\tUNITE: General Fasta release 8.0 for Fungi\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+unite_8.0_fungi_singletons\tUNITE: General Fasta release 8.0 for Fungi including global and 97% singletons\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+RefSeq_RDP_2018_05\tNCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+gtdb_202_toGenus\tGTDB Version 202 to Genus (for short reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_202_toGenus.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+gtdb_202_toSpecies\tGTDB Version 202 to Species (for long reads)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_202_toSpecies.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+gtdb_2018_11\tGTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+hitdb_1\tHitDB version 1 (Human InTestinal 16S rRNA)\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+silva_euk_18S_132\tSilva version 132 Eukaryotic 18S\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy\tKingdom,Phylum,Class,Order,Family,Genus,Species\n+PR2_4.11.1\tProtist Ribosomal Reference database (PR2) 4.11.1\t/tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy\tKingdom,Supergroup,Division,Class,Order,Family,Genus,Species\n' |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/greengenes13.84_json --- a/test-data/greengenes13.84_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/greengenes13.84_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "GreenGenes version 13.84", "path": "greengenes_13.84.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "greengenes_13.84"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "greengenes_13.84", + "name": "GreenGenes version 13.84", + "path": "greengenes_13.84.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/gtdb2018_json --- a/test-data/gtdb2018_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/gtdb2018_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_taxonomy": {"name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", "path": "gtdb_2018_11.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "gtdb_2018_11"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "gtdb_2018_11", + "name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", + "path": "gtdb_2018_11.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "gtdb_2018_11", + "name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", + "path": "gtdb_2018_11.species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/hitdb1_json --- a/test-data/hitdb1_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/hitdb1_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "HitDB version 1 (Human InTestinal 16S rRNA)", "path": "hitdb_1.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "hitdb_1"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "hitdb_1", + "name": "HitDB version 1 (Human InTestinal 16S rRNA)", + "path": "hitdb_1.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/rdp16_json --- a/test-data/rdp16_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/rdp16_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_species": {"name": "RDP trainset 16", "path": "rdp_16.species", "value": "rdp_16"}, "dada2_taxonomy": {"name": "RDP trainset 16", "path": "rdp_16.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "rdp_16"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "rdp_16", + "name": "RDP trainset 16", + "path": "rdp_16.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "rdp_16", + "name": "RDP trainset 16", + "path": "rdp_16.species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/silva132_json --- a/test-data/silva132_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/silva132_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_species": {"name": "Silva version 132", "path": "silva_132.species", "value": "silva_132"}, "dada2_taxonomy": {"name": "Silva version 132", "path": "silva_132.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_132"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "silva_132", + "name": "Silva version 132", + "path": "silva_132.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "silva_132", + "name": "Silva version 132", + "path": "silva_132.species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/silva138_json --- a/test-data/silva138_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/silva138_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_species": {"name": "Silva version 138", "path": "silva_138.species", "value": "silva_138"}, "dada2_taxonomy": {"name": "Silva version 138", "path": "silva_138.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_138"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "silva_138", + "name": "Silva version 138", + "path": "silva_138.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "silva_138", + "name": "Silva version 138", + "path": "silva_138.species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/silvaeuk132_json --- a/test-data/silvaeuk132_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/silvaeuk132_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "Silva version 132 Eukaryotic 18S", "path": "silva_euk_18S_132.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_euk_18S_132"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "silva_euk_18S_132", + "name": "Silva version 132 Eukaryotic 18S", + "path": "silva_euk_18S_132.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/unite8fungi_json --- a/test-data/unite8fungi_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/unite8fungi_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "UNITE: General Fasta release 8.0 for Fungi", "path": "unite_8.0_fungi.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "unite_8.0_fungi"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "unite_8.0_fungi", + "name": "UNITE: General Fasta release 8.0 for Fungi", + "path": "unite_8.0_fungi.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +} |
| b |
| diff -r 678176bff643 -r 0181efacb40a test-data/unite8fungisingletons_json --- a/test-data/unite8fungisingletons_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/unite8fungisingletons_json Sat Nov 22 20:07:44 2025 +0000 |
| [ |
| @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", "path": "unite_8.0_fungi_singletons.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "unite_8.0_fungi_singletons"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "unite_8.0_fungi_singletons", + "name": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", + "path": "unite_8.0_fungi_singletons.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +} |