Mercurial > repos > iuc > data_manager_dada2

annotate data_manager/dada2_fetcher.xml @ 8:b84aace42ca8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
author iuc
date Fri, 12 Dec 2025 09:06:55 +0000
parents cd817c959692
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
1 <tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.3" profile="24.2">
6
2e7c3f0f2c6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 27be397d903081b2e7848e568c587917e4f49b89
iuc
parents: 5
diff changeset
2 <description>Download reference databases</description>
1
e2ad7330a977 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
iuc
parents: 0
diff changeset
3 <requirements>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
4 <requirement type="package" version="1.25.0">wget</requirement>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
5 <requirement type="package" version="6.0">unzip</requirement>
1
e2ad7330a977 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
iuc
parents: 0
diff changeset
6 </requirements>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
8 ## see https://github.com/benjjneb/dada2/issues/2053 for the distinction of the _toGenus and _toSpecies datasets
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
9 #set $FILE2TAXURL = {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
10 "silva_138.2_toGenus": "https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toGenus_trainset.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
11 "silva_138.2_toSpecies": "https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toSpecies_trainset.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
12
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
13 "silva_138.2_fungi_18S_toGenus": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_nr99_v138_2_toGenus_trainset.fasta?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
14 "silva_138.2_fungi_18S_toSpecies": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_nr99_v138_2_toSpecies_trainset.fasta?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
15
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
16 "silva_138.2_fungi_26S_toGenus": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_nr99_v138_2_toGenus_trainset.fasta?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
17 "silva_138.2_fungi_26S_toSpecies": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_nr99_v138_2_toSpecies_trainset.fasta?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
18
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
19 "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
20 "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
21 "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
22 "rdp_19_toGenus": "https://zenodo.org/records/14168771/files/rdp_19_toGenus_trainset.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
23 "rdp_19_toSpecies": "https://zenodo.org/records/14168771/files/rdp_19_toSpecies_trainset.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
24 "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
25 "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
8
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
26 "unite_10.0_eukaryotes-2025-02-19": "https://s3.hpc.ut.ee/plutof-public/original/e861a3d6-54f4-42dc-882a-5f129beac39a.tgz",
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
27 "unite_10.0_eukaryotes_singletons-2025-02-19": "https://s3.hpc.ut.ee/plutof-public/original/b02db549-5f04-43fc-afb6-02888b594d10.tgz",
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
28 "unite_8.0_fungi": "https://s3.hpc.ut.ee/plutof-public/original/9f7b41c3-825b-4db8-9c52-74a4603a860a.zip",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
29 "unite_8.0_fungi_singletons": "https://s3.hpc.ut.ee/plutof-public/original/53dfc9ce-9cb5-4205-84bb-f47faff26462.zip",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
30 "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
31 "greengenes2_2024.09_toGenus": "https://zenodo.org/records/14169078/files/gg2_2024_09_toGenus_trainset.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
32 "greengenes2_2024.09_toSpecies": "https://zenodo.org/records/14169078/files/gg2_2024_09_toSpecies_trainset.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
33 "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
34
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
35 "gtdb_202_toGenus": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_Genus.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
36 "gtdb_202_toSpecies": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_Species.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
37 "gtdb_2018_11": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
38
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
39 "hitdb_1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
40 "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
41 "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz"
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
42 }
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
43 ## rdp_19 not available for assignSpecies https://github.com/benjjneb/dada2/issues/2053#issuecomment-2512185929
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
44 #set FILE2SPECIESURL = {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
45 "silva_138.2": "https://zenodo.org/records/14169026/files/silva_v138.2_assignSpecies.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
46 "silva_138.2_fungi_18S": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_assignSpecies.fasta?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
47 "silva_138.2_fungi_26S": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_assignSpecies.fasta?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
48 "silva_138": "https://zenodo.org/record/3731176/files/silva_species_assignment_v138.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
49 "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
50 "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
51 "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
52 "rdp_14": "https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
53 "gtdb_202": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_fullTaxo.fa.gz?download=1",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
54 "gtdb_2018_11": "https://zenodo.org/records/2658728/files/GTDB_dada2_assignment_species.fa.gz?download=1"
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
55 }
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
56 mkdir -p '${out_file.extra_files_path}' &&
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
57 cd '${out_file.extra_files_path}' &&
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
58 #for $database in $taxonomy_databases:
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
59 wget '$FILE2TAXURL[str($database)]' -O '${database}.taxonomy' &&
8
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
60 #if str($database).startswith("unite_8.0")
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
61 unzip -p '${database}.taxonomy' "*.fasta" -x "developer/*" > tmp &&
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
62 mv tmp '${database}.taxonomy' &&
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
63 #end if
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
64 #end for
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
65 #if $species_databases
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
66 #for $database in $species_databases:
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
67 wget '$FILE2SPECIESURL[str($database)]' -O '${database}.species' &&
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
68 #end for
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
69 #end if
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
70 cp '$dmjson' '$out_file'
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
71 ]]>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
72 </command>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
73 <configfiles>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
74 <configfile name="dmjson"><![CDATA[#slurp
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
75 #set FILE2NAME = {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
76 "silva_138.2_toGenus": "Silva version 138.2 to Genus (for short reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
77 "silva_138.2_toSpecies": "Silva version 138.2 to Species (for long reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
78 "silva_138.2": "Silva version 138.2",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
79
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
80 "silva_138.2_fungi_18S_toGenus": "Silva version 138.2 for Fungi 18S to Genus (for short reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
81 "silva_138.2_fungi_18S_toSpecies": "Silva version 138.2 for Fungi 18S to Species (for long reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
82 "silva_138.2_fungi_18S": "Silva version 138.2 for Fungi 18S",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
83
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
84 "silva_138.2_fungi_26S_toGenus": "Silva version 138.2 for Fungi 26S to Genus (for short reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
85 "silva_138.2_fungi_26S_toSpecies": "Silva version 138.2 for Fungi 26S to Species (for long reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
86 "silva_138.2_fungi_26S": "Silva version 138.2 for Fungi 26S",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
87
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
88 "silva_138": "Silva version 138",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
89 "silva_132": "Silva version 132",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
90 "silva_128": "Silva version 128",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
91 "rdp_19_toGenus": "RDP trainset 19 to Genus (for short reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
92 "rdp_19_toSpecies": "RDP trainset 19 to Species (for long reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
93 "rdp_16": "RDP trainset 16",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
94 "rdp_14": "RDP trainset 14",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
95 "greengenes_13.84": "GreenGenes version 13.84",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
96 "greengenes2_2024.09_toGenus": "GreenGenes2 release 2024.09 to Genus (for short reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
97 "greengenes2_2024.09_toSpecies": "GreenGenes2 release 2024.09 to Species (for long reads)",
8
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
98 "unite_10.0_eukaryotes-2025-02-19": "UNITE: General Fasta release 10.0 (2025-02-19) for Eukaroyes",
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
99 "unite_10.0_eukaryotes_singletons-2025-02-19": "UNITE: General Fasta release 10.0 (2025-02-19) for Eukaroyes including global and 97% singletons",
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
100 "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
101 "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
102 "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
103
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
104 "gtdb_202_toGenus": "GTDB Version 202 to Genus (for short reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
105 "gtdb_202_toSpecies": "GTDB Version 202 to Species (for long reads)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
106 "gtdb_202": "GTDB Version 202",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
107
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
108 "gtdb_2018_11": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
109 "hitdb_1": "HitDB version 1 (Human InTestinal 16S rRNA)",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
110 "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
111 "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1"
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
112 }
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
113 #set FILE2TAXLEVELS = {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
114 "PR2_4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
115 }
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
116 {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
117 "data_tables":{
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
118 "dada2_taxonomy": [
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
119 #for $i, $database in enumerate($taxonomy_databases):
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
120 #set taxlevels = FILE2TAXLEVELS.get(str($database), "Kingdom,Phylum,Class,Order,Family,Genus,Species")
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
121 {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
122 "value": "$database",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
123 "name": "$FILE2NAME[str($database)]",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
124 "path": "${database}.taxonomy",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
125 "taxlevels": "$taxlevels"
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
126 }#slurp
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
127 #if i + 1 < len(str($taxonomy_databases).split(","))
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
128 ,
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
129 #end if
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
130 #end for
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
131 ]
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
132 #if $species_databases
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
133 , "dada2_species": [
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
134 #for $i, $database in enumerate($species_databases):
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
135 {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
136 "value": "$database",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
137 "name": "$FILE2NAME[str($database)]",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
138 "path": "${database}.species"
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
139 }#slurp
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
140 #if i + 1 < len(str($species_databases).split(","))
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
141 ,
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
142 #end if
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
143 #end for
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
144 ]
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
145 #end if
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
146 }
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
147 }
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
148 ]]></configfile>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
149 </configfiles>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
150 <inputs>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
151 <param name="taxonomy_databases" multiple="true" type="select" label="Taxonomic database" help="for assignTaxonomy">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
152 <option value="silva_138.2_toGenus">Silva 138.2 to Genus (for short reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
153 <option value="silva_138.2_toSpecies">Silva 138.2 to Species (for long reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
154
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
155 <option value="silva_138.2_fungi_18S_toGenus">Silva 138.2 for Fungi 18S to Genus (for short reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
156 <option value="silva_138.2_fungi_18S_toSpecies">Silva 138.2 for Fungi 18S to Species (for long read)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
157
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
158 <option value="silva_138.2_fungi_26S_toGenus">Silva 138.2 for Fungi 26S to Genus (for short reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
159 <option value="silva_138.2_fungi_26S_toSpecies">Silva 138.2 for Fungi 26S to Species (for long reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
160
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
161 <option value="silva_138">Silva 138</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
162 <option value="silva_132">Silva 132</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
163 <option value="silva_128">Silva 128</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
164 <option value="rdp_19_toGenus">RDP 19 to Genus (for short reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
165 <option value="rdp_19_toSpecies">RDP 19 to Species (for long reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
166 <option value="rdp_16">RDP 16</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
167 <option value="rdp_14">RDP 14</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
168 <option value="greengenes2_2024.09_toGenus">GreenGenes2 2024.09 to Genus (for short reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
169 <option value="greengenes2_2024.09_toSpecies">GreenGenes2 2024.09 to Species (for long reads)</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
170 <option value="greengenes_13.84">GreenGenes 13.84</option>
8
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
171 <option value="unite_10.0_eukaryotes-2025-02-19">UNITE General Fasta 10.0 (2025-02-19) for Eukaryota</option>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
172 <option value="unite_10.0_eukaryotes_singletons-2025-02-19">UNITE: General Fasta release 10.0 (2025-02-19) for Eukaryota including global and 97% singletons</option>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
173 <option value="unite_8.0_fungi">UNITE: General Fasta 8.0 for Fungi</option>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
174 <option value="unite_8.0_fungi_singletons">UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons</option>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
175 <!-- UNITE Eukaryotes not yet supported https://github.com/benjjneb/dada2/issues/702 -->
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
176 <option value="RefSeq_RDP_2018_05">NCBI RefSeq 16S rRNA database supplemented by RDP 05/2018</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
177 <option value="gtdb_202_toGenus">GTDB: Genome Taxonomy Database 202 to Genus (for short reads) </option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
178 <option value="gtdb_202_toSpecies">GTDB: Genome Taxonomy Database 202 to Species (for long reads) </option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
179 <option value="gtdb_2018_11">GTDB: Genome Taxonomy Database 11/2018</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
180 <option value="hitdb_1">HitDB (Human InTestinal 16S) 1</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
181 <option value="silva_euk_18S_132">Silva Eukaryotic 18S 132</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
182 <option value="PR2_4.11.1">Protist Ribosomal Reference database (PR2) 4.11.1</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
183 </param>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
184 <param name="species_databases" type="select" multiple="true" optional="true" label="Species databases" help="for addSpecies">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
185 <option value="silva_138.2">Silva 138.2</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
186 <option value="silva_138.2_fungi_18S">Silva 138.2 for Fungi 18S</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
187 <option value="silva_138.2_fungi_26S">Silva 138.2 for Fungi 26S</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
188 <option value="silva_138">Silva 138</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
189 <option value="silva_132">Silva 132</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
190 <option value="silva_128">Silva 128</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
191 <option value="rdp_16">RDP 16</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
192 <option value="rdp_14">RDP 14</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
193 <option value="gtdb_202">GTDB: Genome Taxonomy Database 202</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
194 <option value="gtdb_2018_11">GTDB: Genome Taxonomy Database 11/2018</option>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
195 </param>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
196 </inputs>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
197 <outputs>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
198 <data name="out_file" format="data_manager_json" />
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
199 </outputs>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
200 <tests>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
201 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
202 <param name="taxonomy_databases" value="silva_138.2_toGenus,silva_138.2_toSpecies"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
203 <param name="species_databases" value="silva_138.2"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
204 <output name="out_file">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
205 <assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
206 <has_text text="&quot;Silva version 138.2 to Genus (for short reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
207 <has_text text="&quot;Silva version 138.2 to Species (for long reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
208 <has_text text="&quot;Silva version 138.2&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
209 </assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
210 </output>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
211 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
212 <has_text text="wget" n="3"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
213 </assert_command>
5
658dbcc9d77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit fc58a4442c97181cd562761301dffdf6bbf575a5"
iuc
parents: 3
diff changeset
214 </test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
215
5
658dbcc9d77d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit fc58a4442c97181cd562761301dffdf6bbf575a5"
iuc
parents: 3
diff changeset
216 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
217 <param name="taxonomy_databases" value="silva_138.2_fungi_18S_toGenus,silva_138.2_fungi_18S_toSpecies"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
218 <param name="species_databases" value="silva_138.2_fungi_18S"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
219 <output name="out_file">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
220 <assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
221 <has_text text="&quot;Silva version 138.2 for Fungi 18S to Genus (for short reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
222 <has_text text="&quot;Silva version 138.2 for Fungi 18S to Species (for long reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
223 <has_text text="&quot;Silva version 138.2 for Fungi 18S&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
224 </assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
225 </output>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
226 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
227 <has_text text="wget" n="3"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
228 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
229 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
230 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
231 <param name="taxonomy_databases" value="silva_138.2_fungi_26S_toGenus,silva_138.2_fungi_26S_toSpecies"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
232 <param name="species_databases" value="silva_138.2_fungi_26S"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
233 <output name="out_file">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
234 <assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
235 <has_text text="&quot;Silva version 138.2 for Fungi 26S to Genus (for short reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
236 <has_text text="&quot;Silva version 138.2 for Fungi 26S to Species (for long reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
237 <has_text text="&quot;Silva version 138.2 for Fungi 26S&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
238 </assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
239 </output>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
240 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
241 <has_text text="wget" n="3"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
242 </assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
243 </test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
244
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
245 <test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
246 <param name="taxonomy_databases" value="silva_138"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
247 <param name="species_databases" value="silva_138"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
248 <output name="out_file" file="silva138_json"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
249 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
250 <has_text text="wget" n="2"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
251 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
252 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
253 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
254 <param name="taxonomy_databases" value="silva_132"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
255 <param name="species_databases" value="silva_132"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
256 <output name="out_file" file="silva132_json"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
257 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
258 <has_text text="wget" n="2"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
259 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
260 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
261 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
262 <param name="taxonomy_databases" value="rdp_19_toSpecies,rdp_19_toGenus"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
263 <output name="out_file">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
264 <assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
265 <has_text text="RDP trainset 19 to Species (for long reads)"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
266 <has_text text="RDP trainset 19 to Genus (for short reads)"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
267 </assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
268 </output>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
269 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
270 <has_text text="wget" n="2"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
271 </assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
272 </test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
273 <test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
274 <param name="taxonomy_databases" value="rdp_16"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
275 <param name="species_databases" value="rdp_16"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
276 <output name="out_file" file="rdp16_json"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
277 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
278 <has_text text="wget" n="2"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
279 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
280 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
281 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
282 <param name="taxonomy_databases" value="greengenes2_2024.09_toSpecies,greengenes2_2024.09_toGenus"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
283 <output name="out_file">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
284 <assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
285 <has_text text="GreenGenes2 release 2024.09 to Genus (for short reads)"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
286 <has_text text="GreenGenes2 release 2024.09 to Species (for long reads)"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
287 </assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
288 </output>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
289 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
290 <has_text text="wget" n="2"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
291 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
292 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
293 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
294 <param name="taxonomy_databases" value="greengenes_13.84"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
295 <output name="out_file" file="greengenes13.84_json"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
296 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
297 <has_text text="wget" n="1"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
298 </assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
299 </test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
300 <test>
8
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
301 <param name="taxonomy_databases" value="unite_10.0_eukaryotes-2025-02-19"/>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
302 <output name="out_file">
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
303 <assert_contents>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
304 <has_text text='"value": "unite_10.0_eukaryotes-2025-02-19"'/>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
305 </assert_contents>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
306 </output>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
307 <assert_command>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
308 <has_text text="wget" n="1"/>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
309 <has_text text="unzip" negate="true"/>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
310 </assert_command>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
311 </test>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
312 <test>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
313 <param name="taxonomy_databases" value="unite_10.0_eukaryotes_singletons-2025-02-19"/>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
314 <output name="out_file">
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
315 <assert_contents>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
316 <has_text text='"value": "unite_10.0_eukaryotes_singletons-2025-02-19"'/>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
317 </assert_contents>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
318 </output>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
319 <assert_command>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
320 <has_text text="wget" n="1"/>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
321 </assert_command>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
322 </test>
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
323
b84aace42ca8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
iuc
parents: 7
diff changeset
324 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
325 <param name="taxonomy_databases" value="unite_8.0_fungi"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
326 <output name="out_file" file="unite8fungi_json"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
327 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
328 <has_text text="unzip"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
329 </assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
330 </test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
331 <test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
332 <param name="taxonomy_databases" value="unite_8.0_fungi_singletons"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
333 <output name="out_file" file="unite8fungisingletons_json"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
334 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
335 <has_text text="wget" n="1"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
336 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
337 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
338 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
339 <param name="taxonomy_databases" value="RefSeq_RDP_2018_05"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
340 <output name="out_file" file="RefSeq_RDP2018_json"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
341 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
342 <has_text text="wget" n="1"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
343 </assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
344 </test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
345
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
346 <test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
347 <param name="taxonomy_databases" value="gtdb_202_toGenus,gtdb_202_toSpecies"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
348 <param name="species_databases" value="gtdb_202"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
349 <output name="out_file">
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
350 <assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
351 <has_text text="&quot;GTDB Version 202 to Genus (for short reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
352 <has_text text="&quot;GTDB Version 202 to Species (for long reads)&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
353 <has_text text="&quot;GTDB Version 202&quot;"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
354 </assert_contents>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
355 </output>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
356 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
357 <has_text text="wget" n="3"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
358 </assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
359 </test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
360
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
361 <test>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
362 <param name="taxonomy_databases" value="gtdb_2018_11"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
363 <param name="species_databases" value="gtdb_2018_11"/>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
364 <output name="out_file" file="gtdb2018_json"/>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
365 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
366 <has_text text="wget" n="2"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
367 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
368 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
369 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
370 <param name="taxonomy_databases" value="hitdb_1"/>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
371 <output name="out_file" file="hitdb1_json"/>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
372 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
373 <has_text text="wget" n="1"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
374 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
375 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
376 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
377 <param name="taxonomy_databases" value="silva_euk_18S_132"/>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
378 <output name="out_file" file="silvaeuk132_json"/>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
379 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
380 <has_text text="wget" n="1"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
381 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
382 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
383 <test>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
384 <param name="taxonomy_databases" value="PR2_4.11.1"/>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
385 <output name="out_file" file="PR24.11.1_json"/>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
386 <assert_command>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
387 <has_text text="wget" n="1"/>
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
388 </assert_command>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
389 </test>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
390 </tests>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
391 <help><![CDATA[
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
392 Public Reference databases maintained by the DADA2 project
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
393 ..........................................................
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
394
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
395 The following refrence databases which are describes as maintained by the DADA2 project (https://benjjneb.github.io/dada2/training.html) are available
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
396
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
397 - Silva
6
2e7c3f0f2c6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 27be397d903081b2e7848e568c587917e4f49b89
iuc
parents: 5
diff changeset
398 - RDP
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
399 - GreenGenes (https://web.archive.org/web/20240703054246/https://greengenes.secondgenome.com/)
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
400 - Greengenes2 (https://greengenes2.ucsd.edu/)
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
401 - UNITE general FASTA (https://unite.ut.ee/repository.php)
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
402
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
403 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.
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
404
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
405 Silva are licensed under Create Commons Attribution 4.0 (CC-BY 4.0) since release 138.
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
406
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
407 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
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
408
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
409 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html.
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
410
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
411 Further public Reference databases listed by the DADA2 project
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
412 ..............................................................
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
413
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
414 Several contributed reference databases are listed of the DADA2 project website (https://benjjneb.github.io/dada2/training.html):
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
415
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
416 - RefSeq + RDP (NCBI RefSeq 16S rRNA database supplemented by RDP)
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
417 - GTDB: Genome Taxonomy Database (More info: http://gtdb.ecogenomic.org/)
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
418 - HitDB version 1 (Human InTestinal 16S rRNA) (https://github.com/microbiome/HITdb)
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
419 - RDP fungi LSU
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
420 - Silva Eukaryotic 18S
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
421 - PR2 (https://github.com/pr2database/pr2database)
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
422
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
423 Except for PR2, all reference databases are downloaded from the corresponding zenodo links that are listed on the DADA2 website. The PR2 database is taken from their github page.
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
424
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
425 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html.
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
426 ]]></help>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
427 <citations>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
428 <!-- silva -->
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
429 <citation type="doi">10.1093/nar/gks1219</citation>
6
2e7c3f0f2c6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 27be397d903081b2e7848e568c587917e4f49b89
iuc
parents: 5
diff changeset
430 <!-- rdp -->
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
431 <citation type="doi">10.1093/nar/gkt1244</citation>
7
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
432 <!-- greengenes2 -->
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
iuc
parents: 6
diff changeset
433 <citation type="doi">10.1038/s41587-023-01845-1</citation>
0
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
434 <!-- greengenes -->
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
435 <citation type="doi">10.1128/AEM.03006-05</citation>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
436 <!-- unite -->
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
437 <citation type="doi">10.15156/BIO/786343</citation>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
438 <!-- TODO gtdb ??? -->
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
439 <!-- hitdb -->
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
440 <citation type="doi">10.1186/s12864-015-2265-y</citation>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
441 <!-- PR2 -->
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
442 <citation type="doi">10.1093/nar/gks1160</citation>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
443 </citations>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
444 </tool>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
445