Mercurial > repos > iuc > data_manager_dada2

comparison data_manager/data_manager.py @ 2:a6a81f921701 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit a096d3eb593edee6cb08247be3a09138d088a6ce"
author iuc
date Sun, 29 Mar 2020 17:51:21 -0400
parents bf7b2c14cabc
children c29275496061
comparison
equal deleted inserted replaced
1:bf7b2c14cabc 2:a6a81f921701
9 from urllib2 import Request, urlopen 9 from urllib2 import Request, urlopen
10 10
11 DEFAULT_TAXLEVELS = "Kingdom,Phylum,Class,Order,Family,Genus,Species" 11 DEFAULT_TAXLEVELS = "Kingdom,Phylum,Class,Order,Family,Genus,Species"
12 12
13 FILE2NAME = { 13 FILE2NAME = {
14 "silva_138": "Silva version 138",
14 "silva_132": "Silva version 132", 15 "silva_132": "Silva version 132",
15 "silva_128": "Silva version 128", 16 "silva_128": "Silva version 128",
16 "rdp_16": "RDP trainset 16", 17 "rdp_16": "RDP trainset 16",
17 "rdp_14": "RDP trainset 14", 18 "rdp_14": "RDP trainset 14",
18 "greengenes_13.84": "GreenGenes version 13.84", 19 "greengenes_13.84": "GreenGenes version 13.84",
24 "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S", 25 "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S",
25 "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1" 26 "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1"
26 } 27 }
27 28
28 FILE2TAXURL = { 29 FILE2TAXURL = {
30 "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1",
29 "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1", 31 "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1",
30 "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", 32 "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
31 "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", 33 "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
32 "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1", 34 "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
33 "unite_8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip", 35 "unite_8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip",
39 "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1", 41 "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1",
40 "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz" 42 "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz"
41 } 43 }
42 44
43 FILE2SPECIESURL = { 45 FILE2SPECIESURL = {
46 "silva_138": "https://zenodo.org/record/3731176/files/silva_species_assignment_v138.fa.gz?download=1",
44 "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1", 47 "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1",
45 "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1", 48 "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1",
46 "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1", 49 "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1",
47 "rdp_14": "https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1" 50 "rdp_14": "https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1"
48 } 51 }