Mercurial > repos > iuc > data_manager_dada2
changeset 8:0181efacb40a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db
| author | iuc |
|---|---|
| date | Sat, 22 Nov 2025 20:07:44 +0000 |
| parents | 678176bff643 |
| children | |
| files | data_manager/dada2_fetcher.xml data_manager/data_manager.py test-data/PR24.11.1_json test-data/RefSeq_RDP2018_json test-data/dada2_species.loc test-data/dada2_taxonomy.loc test-data/greengenes13.84_json test-data/gtdb2018_json test-data/hitdb1_json test-data/rdp16_json test-data/silva132_json test-data/silva138_json test-data/silvaeuk132_json test-data/unite8fungi_json test-data/unite8fungisingletons_json |
| diffstat | 15 files changed, 798 insertions(+), 249 deletions(-) [+] |
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--- a/data_manager/dada2_fetcher.xml Tue May 21 07:35:56 2024 +0000 +++ b/data_manager/dada2_fetcher.xml Sat Nov 22 20:07:44 2025 +0000 @@ -1,139 +1,361 @@ -<?xml version="1.0"?> -<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.1" profile="23.0"> +<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.2" profile="24.2"> <description>Download reference databases</description> <requirements> - <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="1.25.0">wget</requirement> + <requirement type="package" version="6.0">unzip</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - python '$__tool_directory__/data_manager.py' - --out '$out_file' - #set dataset = str($db_cond.db_select) + '_' + str($db_cond.version_select) - --dataset '$dataset' +## see https://github.com/benjjneb/dada2/issues/2053 for the distinction of the _toGenus and _toSpecies datasets +#set $FILE2TAXURL = { + "silva_138.2_toGenus": "https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toGenus_trainset.fa.gz?download=1", + "silva_138.2_toSpecies": "https://zenodo.org/records/14169026/files/silva_nr99_v138.2_toSpecies_trainset.fa.gz?download=1", + + "silva_138.2_fungi_18S_toGenus": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_nr99_v138_2_toGenus_trainset.fasta?download=1", + "silva_138.2_fungi_18S_toSpecies": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_nr99_v138_2_toSpecies_trainset.fasta?download=1", + + "silva_138.2_fungi_26S_toGenus": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_nr99_v138_2_toGenus_trainset.fasta?download=1", + "silva_138.2_fungi_26S_toSpecies": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_nr99_v138_2_toSpecies_trainset.fasta?download=1", + + "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1", + "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1", + "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", + "rdp_19_toGenus": "https://zenodo.org/records/14168771/files/rdp_19_toGenus_trainset.fa.gz?download=1", + "rdp_19_toSpecies": "https://zenodo.org/records/14168771/files/rdp_19_toSpecies_trainset.fa.gz?download=1", + "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", + "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1", + "unite_8.0_fungi": "https://s3.hpc.ut.ee/plutof-public/original/9f7b41c3-825b-4db8-9c52-74a4603a860a.zip", + "unite_8.0_fungi_singletons": "https://s3.hpc.ut.ee/plutof-public/original/53dfc9ce-9cb5-4205-84bb-f47faff26462.zip", + "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1", + "greengenes2_2024.09_toGenus": "https://zenodo.org/records/14169078/files/gg2_2024_09_toGenus_trainset.fa.gz?download=1", + "greengenes2_2024.09_toSpecies": "https://zenodo.org/records/14169078/files/gg2_2024_09_toSpecies_trainset.fa.gz?download=1", + "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1", + + "gtdb_202_toGenus": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_Genus.fa.gz?download=1", + "gtdb_202_toSpecies": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_Species.fa.gz?download=1", + "gtdb_2018_11": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1", + + "hitdb_1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1", + "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1", + "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz" +} +## rdp_19 not available for assignSpecies https://github.com/benjjneb/dada2/issues/2053#issuecomment-2512185929 +#set FILE2SPECIESURL = { + "silva_138.2": "https://zenodo.org/records/14169026/files/silva_v138.2_assignSpecies.fa.gz?download=1", + "silva_138.2_fungi_18S": "https://zenodo.org/records/15044434/files/SILVA_SSUfungi_assignSpecies.fasta?download=1", + "silva_138.2_fungi_26S": "https://zenodo.org/records/15044501/files/SILVA_LSUfungi_assignSpecies.fasta?download=1", + "silva_138": "https://zenodo.org/record/3731176/files/silva_species_assignment_v138.fa.gz?download=1", + "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1", + "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1", + "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1", + "rdp_14": "https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1", + "gtdb_202": "https://zenodo.org/records/4735821/files/GTDB_bac120_arc122_ssu_r202_fullTaxo.fa.gz?download=1", + "gtdb_2018_11": "https://zenodo.org/records/2658728/files/GTDB_dada2_assignment_species.fa.gz?download=1" +} +mkdir -p '${out_file.extra_files_path}' && +cd '${out_file.extra_files_path}' && +#for $database in $taxonomy_databases: + wget '$FILE2TAXURL[str($database)]' -O '${database}.taxonomy' && + #if str($database).startswith("unite") + unzip -p '${database}.taxonomy' "*.fasta" -x "developer/*" > tmp && + mv tmp '${database}.taxonomy' && + #end if +#end for +#if $species_databases + #for $database in $species_databases: + wget '$FILE2SPECIESURL[str($database)]' -O '${database}.species' && + #end for +#end if + cp '$dmjson' '$out_file' ]]> </command> + <configfiles> + <configfile name="dmjson"><![CDATA[#slurp +#set FILE2NAME = { + "silva_138.2_toGenus": "Silva version 138.2 to Genus (for short reads)", + "silva_138.2_toSpecies": "Silva version 138.2 to Species (for long reads)", + "silva_138.2": "Silva version 138.2", + + "silva_138.2_fungi_18S_toGenus": "Silva version 138.2 for Fungi 18S to Genus (for short reads)", + "silva_138.2_fungi_18S_toSpecies": "Silva version 138.2 for Fungi 18S to Species (for long reads)", + "silva_138.2_fungi_18S": "Silva version 138.2 for Fungi 18S", + + "silva_138.2_fungi_26S_toGenus": "Silva version 138.2 for Fungi 26S to Genus (for short reads)", + "silva_138.2_fungi_26S_toSpecies": "Silva version 138.2 for Fungi 26S to Species (for long reads)", + "silva_138.2_fungi_26S": "Silva version 138.2 for Fungi 26S", + + "silva_138": "Silva version 138", + "silva_132": "Silva version 132", + "silva_128": "Silva version 128", + "rdp_19_toGenus": "RDP trainset 19 to Genus (for short reads)", + "rdp_19_toSpecies": "RDP trainset 19 to Species (for long reads)", + "rdp_16": "RDP trainset 16", + "rdp_14": "RDP trainset 14", + "greengenes_13.84": "GreenGenes version 13.84", + "greengenes2_2024.09_toGenus": "GreenGenes2 release 2024.09 to Genus (for short reads)", + "greengenes2_2024.09_toSpecies": "GreenGenes2 release 2024.09 to Species (for long reads)", + "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi", + "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", + "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", + + "gtdb_202_toGenus": "GTDB Version 202 to Genus (for short reads)", + "gtdb_202_toSpecies": "GTDB Version 202 to Species (for long reads)", + "gtdb_202": "GTDB Version 202", + + "gtdb_2018_11": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", + "hitdb_1": "HitDB version 1 (Human InTestinal 16S rRNA)", + "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S", + "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1" +} +#set FILE2TAXLEVELS = { + "PR2_4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species", +} +{ + "data_tables":{ + "dada2_taxonomy": [ +#for $i, $database in enumerate($taxonomy_databases): + #set taxlevels = FILE2TAXLEVELS.get(str($database), "Kingdom,Phylum,Class,Order,Family,Genus,Species") + { + "value": "$database", + "name": "$FILE2NAME[str($database)]", + "path": "${database}.taxonomy", + "taxlevels": "$taxlevels" + }#slurp + #if i + 1 < len(str($taxonomy_databases).split(",")) +, + #end if +#end for + ] +#if $species_databases + , "dada2_species": [ +#for $i, $database in enumerate($species_databases): + { + "value": "$database", + "name": "$FILE2NAME[str($database)]", + "path": "${database}.species" + }#slurp + #if i + 1 < len(str($species_databases).split(",")) +, + #end if +#end for + ] +#end if + } +} +]]></configfile> + </configfiles> <inputs> - <conditional name="db_cond"> - <param name="db_select" type="select" label="Taxonomic database"> - <option value="silva">Silva</option> - <option value="rdp">RDP</option> - <option value="greengenes">GreenGenes</option> - <option value="unite">UNITE Fungi: General Fasta</option> - <!-- UNITE Eukaryotes not yet supported https://github.com/benjjneb/dada2/issues/702 --> - <option value="RefSeq_RDP">NCBI RefSeq 16S rRNA database supplemented by RDP</option> - <option value="gtdb">GTDB: Genome Taxonomy Database (Bacteria & Archaea)</option> - <option value="hitdb">HitDB (Human InTestinal 16S)</option> - <option value="silva_euk_18S">Silva Eukaryotic 18S</option> - <option value="PR2">Protist Ribosomal Reference database (PR2)</option> - </param> - <when value="silva"> - <param name="version_select" type="select" label="Database version"> - <option value="138">138</option> - <option value="132">132</option> - <option value="128">128</option> - </param> - </when> - <when value="rdp"> - <param name="version_select" type="select" label="Database version"> - <option value="16">16</option> - <option value="14">14</option> - </param> - </when> - <when value="greengenes"> - <param name="version_select" type="select" label="Database version"> - <option value="13.84">13.84</option> - </param> - </when> - <when value="unite"> - <param name="version_select" type="select" label="Database version"> - <option value="8.0_fungi">release 8.0 for Fungi</option> - <option value="8.0_fungi_singletons">release 8.0 for Fungi including global and 97% singletons</option> - </param> - </when> - <when value="RefSeq_RDP"> - <param name="version_select" type="select" label="Database version"> - <option value="2018_05">05/2018</option> - </param> - </when> - <when value="gtdb"> - <param name="version_select" type="select" label="Database version"> - <option value="2018_11">11/2018</option> - </param> - </when> - <when value="hitdb"> - <param name="version_select" type="select" label="Database version"> - <option value="1">1</option> - </param> - </when> - <when value="silva_euk_18S"> - <param name="version_select" type="select" label="Database version"> - <option value="132">132</option> - </param> - </when> - <when value="PR2"> - <param name="version_select" type="select" label="Database version"> - <option value="4.11.1">4.11.1</option> - </param> - </when> - </conditional> + <param name="taxonomy_databases" multiple="true" type="select" label="Taxonomic database" help="for assignTaxonomy"> + <option value="silva_138.2_toGenus">Silva 138.2 to Genus (for short reads)</option> + <option value="silva_138.2_toSpecies">Silva 138.2 to Species (for long reads)</option> + + <option value="silva_138.2_fungi_18S_toGenus">Silva 138.2 for Fungi 18S to Genus (for short reads)</option> + <option value="silva_138.2_fungi_18S_toSpecies">Silva 138.2 for Fungi 18S to Species (for long read)</option> + + <option value="silva_138.2_fungi_26S_toGenus">Silva 138.2 for Fungi 26S to Genus (for short reads)</option> + <option value="silva_138.2_fungi_26S_toSpecies">Silva 138.2 for Fungi 26S to Species (for long reads)</option> + + <option value="silva_138">Silva 138</option> + <option value="silva_132">Silva 132</option> + <option value="silva_128">Silva 128</option> + <option value="rdp_19_toGenus">RDP 19 to Genus (for short reads)</option> + <option value="rdp_19_toSpecies">RDP 19 to Species (for long reads)</option> + <option value="rdp_16">RDP 16</option> + <option value="rdp_14">RDP 14</option> + <option value="greengenes2_2024.09_toGenus">GreenGenes2 2024.09 to Genus (for short reads)</option> + <option value="greengenes2_2024.09_toSpecies">GreenGenes2 2024.09 to Species (for long reads)</option> + <option value="greengenes_13.84">GreenGenes 13.84</option> + <option value="unite_8.0_fungi">UNITE Fungi: General Fasta 8.0 for Fungi</option> + <option value="unite_8.0_fungi_singletons">UNITE Fungi: General Fasta release 8.0 for Fungi including global and 97% singletons</option> + <!-- UNITE Eukaryotes not yet supported https://github.com/benjjneb/dada2/issues/702 --> + <option value="RefSeq_RDP_2018_05">NCBI RefSeq 16S rRNA database supplemented by RDP 05/2018</option> + <option value="gtdb_202_toGenus">GTDB: Genome Taxonomy Database 202 to Genus (for short reads) </option> + <option value="gtdb_202_toSpecies">GTDB: Genome Taxonomy Database 202 to Species (for long reads) </option> + <option value="gtdb_2018_11">GTDB: Genome Taxonomy Database 11/2018</option> + <option value="hitdb_1">HitDB (Human InTestinal 16S) 1</option> + <option value="silva_euk_18S_132">Silva Eukaryotic 18S 132</option> + <option value="PR2_4.11.1">Protist Ribosomal Reference database (PR2) 4.11.1</option> + </param> + <param name="species_databases" type="select" multiple="true" optional="true" label="Species databases" help="for addSpecies"> + <option value="silva_138.2">Silva 138.2</option> + <option value="silva_138.2_fungi_18S">Silva 138.2 for Fungi 18S</option> + <option value="silva_138.2_fungi_26S">Silva 138.2 for Fungi 26S</option> + <option value="silva_138">Silva 138</option> + <option value="silva_132">Silva 132</option> + <option value="silva_128">Silva 128</option> + <option value="rdp_16">RDP 16</option> + <option value="rdp_14">RDP 14</option> + <option value="gtdb_202">GTDB: Genome Taxonomy Database 202</option> + <option value="gtdb_2018_11">GTDB: Genome Taxonomy Database 11/2018</option> + </param> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> <test> - <param name="db_cond|db_select" value="silva"/> - <param name="db_cond|version_select" value="138"/> - <output name="out_file" file="silva138_json"/> + <param name="taxonomy_databases" value="silva_138.2_toGenus,silva_138.2_toSpecies"/> + <param name="species_databases" value="silva_138.2"/> + <output name="out_file"> + <assert_contents> + <has_text text=""Silva version 138.2 to Genus (for short reads)""/> + <has_text text=""Silva version 138.2 to Species (for long reads)""/> + <has_text text=""Silva version 138.2""/> + </assert_contents> + </output> + <assert_command> + <has_text text="wget" n="3"/> + </assert_command> </test> + <test> - <param name="db_cond|db_select" value="silva"/> - <param name="db_cond|version_select" value="132"/> - <output name="out_file" file="silva132_json"/> + <param name="taxonomy_databases" value="silva_138.2_fungi_18S_toGenus,silva_138.2_fungi_18S_toSpecies"/> + <param name="species_databases" value="silva_138.2_fungi_18S"/> + <output name="out_file"> + <assert_contents> + <has_text text=""Silva version 138.2 for Fungi 18S to Genus (for short reads)""/> + <has_text text=""Silva version 138.2 for Fungi 18S to Species (for long reads)""/> + <has_text text=""Silva version 138.2 for Fungi 18S""/> + </assert_contents> + </output> + <assert_command> + <has_text text="wget" n="3"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="rdp"/> - <param name="db_cond|version_select" value="16"/> - <output name="out_file" file="rdp16_json"/> + <param name="taxonomy_databases" value="silva_138.2_fungi_26S_toGenus,silva_138.2_fungi_26S_toSpecies"/> + <param name="species_databases" value="silva_138.2_fungi_26S"/> + <output name="out_file"> + <assert_contents> + <has_text text=""Silva version 138.2 for Fungi 26S to Genus (for short reads)""/> + <has_text text=""Silva version 138.2 for Fungi 26S to Species (for long reads)""/> + <has_text text=""Silva version 138.2 for Fungi 26S""/> + </assert_contents> + </output> + <assert_command> + <has_text text="wget" n="3"/> + </assert_command> + </test> + + <test> + <param name="taxonomy_databases" value="silva_138"/> + <param name="species_databases" value="silva_138"/> + <output name="out_file" file="silva138_json"/> + <assert_command> + <has_text text="wget" n="2"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="greengenes"/> - <param name="db_cond|version_select" value="13.84"/> - <output name="out_file" file="greengenes13.84_json"/> + <param name="taxonomy_databases" value="silva_132"/> + <param name="species_databases" value="silva_132"/> + <output name="out_file" file="silva132_json"/> + <assert_command> + <has_text text="wget" n="2"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="unite"/> - <param name="db_cond|version_select" value="8.0_fungi"/> - <output name="out_file" file="unite8fungi_json"/> + <param name="taxonomy_databases" value="rdp_19_toSpecies,rdp_19_toGenus"/> + <output name="out_file"> + <assert_contents> + <has_text text="RDP trainset 19 to Species (for long reads)"/> + <has_text text="RDP trainset 19 to Genus (for short reads)"/> + </assert_contents> + </output> + <assert_command> + <has_text text="wget" n="2"/> + </assert_command> + </test> + <test> + <param name="taxonomy_databases" value="rdp_16"/> + <param name="species_databases" value="rdp_16"/> + <output name="out_file" file="rdp16_json"/> + <assert_command> + <has_text text="wget" n="2"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="unite"/> - <param name="db_cond|version_select" value="8.0_fungi_singletons"/> - <output name="out_file" file="unite8fungisingletons_json"/> + <param name="taxonomy_databases" value="greengenes2_2024.09_toSpecies,greengenes2_2024.09_toGenus"/> + <output name="out_file"> + <assert_contents> + <has_text text="GreenGenes2 release 2024.09 to Genus (for short reads)"/> + <has_text text="GreenGenes2 release 2024.09 to Species (for long reads)"/> + </assert_contents> + </output> + <assert_command> + <has_text text="wget" n="2"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="RefSeq_RDP"/> - <param name="db_cond|version_select" value="2018_05"/> - <output name="out_file" file="RefSeq_RDP2018_json"/> + <param name="taxonomy_databases" value="greengenes_13.84"/> + <output name="out_file" file="greengenes13.84_json"/> + <assert_command> + <has_text text="wget" n="1"/> + </assert_command> + </test> + <test> + <param name="taxonomy_databases" value="unite_8.0_fungi"/> + <output name="out_file" file="unite8fungi_json"/> + <assert_command> + <has_text text="unzip"/> + </assert_command> + </test> + <test> + <param name="taxonomy_databases" value="unite_8.0_fungi_singletons"/> + <output name="out_file" file="unite8fungisingletons_json"/> + <assert_command> + <has_text text="wget" n="1"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="gtdb"/> - <param name="db_cond|version_select" value="2018_11"/> + <param name="taxonomy_databases" value="RefSeq_RDP_2018_05"/> + <output name="out_file" file="RefSeq_RDP2018_json"/> + <assert_command> + <has_text text="wget" n="1"/> + </assert_command> + </test> + + <test> + <param name="taxonomy_databases" value="gtdb_202_toGenus,gtdb_202_toSpecies"/> + <param name="species_databases" value="gtdb_202"/> + <output name="out_file"> + <assert_contents> + <has_text text=""GTDB Version 202 to Genus (for short reads)""/> + <has_text text=""GTDB Version 202 to Species (for long reads)""/> + <has_text text=""GTDB Version 202""/> + </assert_contents> + </output> + <assert_command> + <has_text text="wget" n="3"/> + </assert_command> + </test> + + <test> + <param name="taxonomy_databases" value="gtdb_2018_11"/> + <param name="species_databases" value="gtdb_2018_11"/> <output name="out_file" file="gtdb2018_json"/> + <assert_command> + <has_text text="wget" n="2"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="hitdb"/> - <param name="db_cond|version_select" value="1"/> + <param name="taxonomy_databases" value="hitdb_1"/> <output name="out_file" file="hitdb1_json"/> + <assert_command> + <has_text text="wget" n="1"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="silva_euk_18S"/> - <param name="db_cond|version_select" value="132"/> + <param name="taxonomy_databases" value="silva_euk_18S_132"/> <output name="out_file" file="silvaeuk132_json"/> + <assert_command> + <has_text text="wget" n="1"/> + </assert_command> </test> <test> - <param name="db_cond|db_select" value="PR2"/> - <param name="db_cond|version_select" value="4.11.1"/> + <param name="taxonomy_databases" value="PR2_4.11.1"/> <output name="out_file" file="PR24.11.1_json"/> + <assert_command> + <has_text text="wget" n="1"/> + </assert_command> </test> </tests> <help><![CDATA[ @@ -142,14 +364,15 @@ The following refrence databases which are describes as maintained by the DADA2 project (https://benjjneb.github.io/dada2/training.html) are available -- Silva (https://www.arb-silva.de/) +- Silva - RDP -- GreenGenes (http://greengenes.secondgenome.com/) +- GreenGenes (https://web.archive.org/web/20240703054246/https://greengenes.secondgenome.com/) +- Greengenes2 (https://greengenes2.ucsd.edu/) - UNITE general FASTA (https://unite.ut.ee/repository.php) 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. -For the Silva databases check the license information: http://www.arb-silva.de/silva-license-information. +Silva are licensed under Create Commons Attribution 4.0 (CC-BY 4.0) since release 138. 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 @@ -176,6 +399,8 @@ <citation type="doi">10.1093/nar/gks1219</citation> <!-- rdp --> <citation type="doi">10.1093/nar/gkt1244</citation> + <!-- greengenes2 --> + <citation type="doi">10.1038/s41587-023-01845-1</citation> <!-- greengenes --> <citation type="doi">10.1128/AEM.03006-05</citation> <!-- unite -->
--- a/data_manager/data_manager.py Tue May 21 07:35:56 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,136 +0,0 @@ -import argparse -import json -import os -try: - # For Python 3.0 and later - from urllib.request import Request, urlopen -except ImportError: - # Fall back to Python 2 imports - from urllib2 import Request, urlopen - -DEFAULT_TAXLEVELS = "Kingdom,Phylum,Class,Order,Family,Genus,Species" - -FILE2NAME = { - "silva_138": "Silva version 138", - "silva_132": "Silva version 132", - "silva_128": "Silva version 128", - "rdp_16": "RDP trainset 16", - "rdp_14": "RDP trainset 14", - "greengenes_13.84": "GreenGenes version 13.84", - "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi", - "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", - "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", - "gtdb_2018_11": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", - "hitdb_1": "HitDB version 1 (Human InTestinal 16S rRNA)", - "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S", - "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1" -} - -FILE2TAXURL = { - "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1", - "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1", - "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", - "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", - "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1", - "unite_8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip", - "unite_8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip", - "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1", - "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1", - "gtdb_2018_11": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1", - "hitdb_1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1", - "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1", - "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz" -} - -FILE2SPECIESURL = { - "silva_138": "https://zenodo.org/record/3731176/files/silva_species_assignment_v138.fa.gz?download=1", - "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1", - "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1", - "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1", - "rdp_14": "https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1" -} - -FILE2TAXLEVELS = { - "PR2_4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species" -} - - -def url_download(url, fname, workdir): - """ - download url to workdir/fname - """ - file_path = os.path.join(workdir, fname) - if not os.path.exists(workdir): - os.makedirs(workdir) - src = None - dst = None - try: - req = Request(url) - src = urlopen(req) - with open(file_path, 'wb') as dst: - while True: - chunk = src.read(2**10) - if chunk: - dst.write(chunk) - else: - break - finally: - if src: - src.close() - -# special treatment of UNITE DBs: they are zip files containing two fasta (xyz.fasta and developer/xyz.fasta) - if fname.startswith("unite"): - import glob - import gzip - import shutil - import zipfile - # unzip download - zip_ref = zipfile.ZipFile(file_path, 'r') - zip_ref.extractall(workdir) - zip_ref.close() - # gzip top level fasta file - fastas = glob.glob("%s/*fasta" % workdir) - if len(fastas) != 1: - msg = "UNITE download %s contained %d fasta file(s): %s" % (url, len(fastas), " ".join(fastas)) - raise Exception(msg) - with open(fastas[0], 'rb') as f_in: - with gzip.open(file_path, 'wb') as f_out: - shutil.copyfileobj(f_in, f_out) - - -def remote_dataset(dataset, outjson): - - with open(outjson) as fh: - params = json.load(fh) - - workdir = params['output_data'][0]['extra_files_path'] - os.mkdir(workdir) - url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir) - - data_manager_json = {"data_tables": {}} - data_manager_entry = {} - data_manager_entry['value'] = dataset - data_manager_entry['name'] = FILE2NAME[dataset] - data_manager_entry['path'] = dataset + ".taxonomy" - data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS) - data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry - - if FILE2SPECIESURL.get(dataset, False): - url_download(FILE2SPECIESURL[dataset], dataset + ".species", workdir) - data_manager_entry = {} - data_manager_entry['value'] = dataset - data_manager_entry['name'] = FILE2NAME[dataset] - data_manager_entry['path'] = dataset + ".species" - data_manager_json["data_tables"]["dada2_species"] = data_manager_entry - - with open(outjson, 'w') as fh: - json.dump(data_manager_json, fh, sort_keys=True) - - -if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Create data manager json.') - parser.add_argument('--out', action='store', help='JSON filename') - parser.add_argument('--dataset', action='store', help='Download data set name') - args = parser.parse_args() - - remote_dataset(args.dataset, args.out)
--- a/test-data/PR24.11.1_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/PR24.11.1_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "Protist Ribosomal Reference database (PR2) 4.11.1", "path": "PR2_4.11.1.taxonomy", "taxlevels": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species", "value": "PR2_4.11.1"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "PR2_4.11.1", + "name": "Protist Ribosomal Reference database (PR2) 4.11.1", + "path": "PR2_4.11.1.taxonomy", + "taxlevels": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species" + } ] + } +}
--- a/test-data/RefSeq_RDP2018_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/RefSeq_RDP2018_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", "path": "RefSeq_RDP_2018_05.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "RefSeq_RDP_2018_05"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "RefSeq_RDP_2018_05", + "name": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", + "path": "RefSeq_RDP_2018_05.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +}
--- a/test-data/dada2_species.loc Tue May 21 07:35:56 2024 +0000 +++ b/test-data/dada2_species.loc Sat Nov 22 20:07:44 2025 +0000 @@ -7,3 +7,62 @@ # Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html # # Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html +silva_138 Silva version 138 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.species +silva_138 Silva version 138 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138 Silva version 138 /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/silva_138.taxonomy +silva_132 Silva version 132 /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/silva_132.taxonomy +rdp_16 RDP trainset 16 /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/rdp_16.taxonomy +silva_138 Silva version 138 /tmp/tmp7bm731ex/galaxy-dev/tool-data/dada2/silva_138.taxonomy +silva_138.2 Silva version 138.2 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_138.2.taxonomy +silva_138 Silva version 138 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_138.taxonomy +silva_132 Silva version 132 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_132.taxonomy +rdp_16 RDP trainset 16 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/rdp_16.taxonomy +silva_138 Silva version 138 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138 Silva version 138 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138 Silva version 138 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138.2 Silva version 138.2 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138 Silva version 138 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138.2 Silva version 138.2 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/rdp_16.species +silva_138.2 Silva version 138.2 /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.species +silva_138.2 Silva version 138.2 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/rdp_16.species +gtdb_202 GTDB Version 202 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/gtdb_202.species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/gtdb_2018_11.species +silva_138.2 Silva version 138.2 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/rdp_16.species +gtdb_202 GTDB Version 202 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/gtdb_202.species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/gtdb_2018_11.species +silva_138.2 Silva version 138.2 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2.species +silva_138.2_fungi_18S Silva version 138.2 for Fungi 18S /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S.species +silva_138.2_fungi_26S Silva version 138.2 for Fungi 26S /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S.species +silva_138 Silva version 138 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.species +silva_132 Silva version 132 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_132.species +rdp_16 RDP trainset 16 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_16.species +gtdb_202 GTDB Version 202 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_202.species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_2018_11.species
--- a/test-data/dada2_taxonomy.loc Tue May 21 07:35:56 2024 +0000 +++ b/test-data/dada2_taxonomy.loc Sat Nov 22 20:07:44 2025 +0000 @@ -7,3 +7,270 @@ # Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html # # taxlevels is a comma separated list of taxonomy levels +silva_138.2_toGenus Silva version 138.2 to Genus (for short read 16S) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long read 16S) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long read 16S) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short read 16S) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short read 16S) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read 16S) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmpwu1f80mk/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy 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/home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /home/berntm/projects/galaxyproject/galaxy/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138 Silva version 138 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Silva version 138 /tmp/tmp7bm731ex/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toGenus Silva version 138.2 to Genus (for short read 16S) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long read 16S) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long read 16S) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short read 16S) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read 16S) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short read 16S) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmpr1gsd54b/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long read 16S) /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short read 16S) /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read 16S) /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short read 16S) /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmpoi2hra5r/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long read 16S) /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short read 16S) /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read 16S) /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short read 16S) /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmp47q48feg/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmp91nggwrv/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toGenus Silva version 138.2 to Genus (for short read 16S) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long read 16S) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long read 16S) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short read 16S) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read 16S) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short read 16S) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmpup9xbr2j/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138.2_toGenus Silva version 138.2 to Genus (for short reads) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long reads) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toGenus Silva version 138.2 for Fungi 18S to Genus (for short reads) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toSpecies Silva version 138.2 for Fungi 18S to Species (for long reads) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toGenus Silva version 138.2 for Fungi 26S to Genus (for short reads) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toSpecies Silva version 138.2 for Fungi 26S to Species (for long reads) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long read 16S) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short read 16S) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read 16S) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short read 16S) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmpxu6le44b/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138.2_toGenus Silva version 138.2 to Genus (for short reads) /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long reads) /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toGenus Silva version 138.2 for Fungi 18S to Genus (for short reads) /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toSpecies Silva version 138.2 for Fungi 18S to Species (for long reads) /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toGenus Silva version 138.2 for Fungi 26S to Genus (for short reads) /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toSpecies Silva version 138.2 for Fungi 26S to Species (for long reads) /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmp6zg8nm9p/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toGenus Silva version 138.2 to Genus (for short reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toGenus Silva version 138.2 for Fungi 18S to Genus (for short reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toSpecies Silva version 138.2 for Fungi 18S to Species (for long reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toGenus Silva version 138.2 for Fungi 26S to Genus (for short reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toSpecies Silva version 138.2 for Fungi 26S to Species (for long reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long read 16S) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short read 16S) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read 16S) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short read 16S) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_202_toGenus GTDB Version 202 to Genus (for short reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/gtdb_202_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_202_toSpecies GTDB Version 202 to Species (for long reads) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/gtdb_202_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmpqhx678py/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138.2_toGenus Silva version 138.2 to Genus (for short reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toGenus Silva version 138.2 for Fungi 18S to Genus (for short reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toSpecies Silva version 138.2 for Fungi 18S to Species (for long reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toGenus Silva version 138.2 for Fungi 26S to Genus (for short reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toSpecies Silva version 138.2 for Fungi 26S to Species (for long reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long read) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_202_toGenus GTDB Version 202 to Genus (for short reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/gtdb_202_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_202_toSpecies GTDB Version 202 to Species (for long reads) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/gtdb_202_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmp69cbfw_6/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species +silva_138.2_toGenus Silva version 138.2 to Genus (for short reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_toSpecies Silva version 138.2 to Species (for long reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toGenus Silva version 138.2 for Fungi 18S to Genus (for short reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_18S_toSpecies Silva version 138.2 for Fungi 18S to Species (for long reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_18S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toGenus Silva version 138.2 for Fungi 26S to Genus (for short reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138.2_fungi_26S_toSpecies Silva version 138.2 for Fungi 26S to Species (for long reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.2_fungi_26S_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_138 Silva version 138 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_138.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_132 Silva version 132 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toSpecies RDP trainset 19 to Species (for long reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_19_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_19_toGenus RDP trainset 19 to Genus (for short reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_19_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +rdp_16 RDP trainset 16 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/rdp_16.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toSpecies GreenGenes2 release 2024.09 to Species (for long reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes2_2024.09_toGenus GreenGenes2 release 2024.09 to Genus (for short reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/greengenes2_2024.09_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +greengenes_13.84 GreenGenes version 13.84 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/greengenes_13.84.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi UNITE: General Fasta release 8.0 for Fungi /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/unite_8.0_fungi.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +unite_8.0_fungi_singletons UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/unite_8.0_fungi_singletons.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +RefSeq_RDP_2018_05 NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/RefSeq_RDP_2018_05.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_202_toGenus GTDB Version 202 to Genus (for short reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_202_toGenus.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_202_toSpecies GTDB Version 202 to Species (for long reads) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_202_toSpecies.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +gtdb_2018_11 GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/gtdb_2018_11.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +hitdb_1 HitDB version 1 (Human InTestinal 16S rRNA) /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/hitdb_1.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +silva_euk_18S_132 Silva version 132 Eukaryotic 18S /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/silva_euk_18S_132.taxonomy Kingdom,Phylum,Class,Order,Family,Genus,Species +PR2_4.11.1 Protist Ribosomal Reference database (PR2) 4.11.1 /tmp/tmpi0_027xn/galaxy-dev/tool-data/dada2/PR2_4.11.1.taxonomy Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species
--- a/test-data/greengenes13.84_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/greengenes13.84_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "GreenGenes version 13.84", "path": "greengenes_13.84.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "greengenes_13.84"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "greengenes_13.84", + "name": "GreenGenes version 13.84", + "path": "greengenes_13.84.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +}
--- a/test-data/gtdb2018_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/gtdb2018_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_taxonomy": {"name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", "path": "gtdb_2018_11.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "gtdb_2018_11"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "gtdb_2018_11", + "name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", + "path": "gtdb_2018_11.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "gtdb_2018_11", + "name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", + "path": "gtdb_2018_11.species" + } ] + } +}
--- a/test-data/hitdb1_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/hitdb1_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "HitDB version 1 (Human InTestinal 16S rRNA)", "path": "hitdb_1.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "hitdb_1"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "hitdb_1", + "name": "HitDB version 1 (Human InTestinal 16S rRNA)", + "path": "hitdb_1.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +}
--- a/test-data/rdp16_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/rdp16_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_species": {"name": "RDP trainset 16", "path": "rdp_16.species", "value": "rdp_16"}, "dada2_taxonomy": {"name": "RDP trainset 16", "path": "rdp_16.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "rdp_16"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "rdp_16", + "name": "RDP trainset 16", + "path": "rdp_16.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "rdp_16", + "name": "RDP trainset 16", + "path": "rdp_16.species" + } ] + } +}
--- a/test-data/silva132_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/silva132_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_species": {"name": "Silva version 132", "path": "silva_132.species", "value": "silva_132"}, "dada2_taxonomy": {"name": "Silva version 132", "path": "silva_132.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_132"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "silva_132", + "name": "Silva version 132", + "path": "silva_132.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "silva_132", + "name": "Silva version 132", + "path": "silva_132.species" + } ] + } +}
--- a/test-data/silva138_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/silva138_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,17 @@ -{"data_tables": {"dada2_species": {"name": "Silva version 138", "path": "silva_138.species", "value": "silva_138"}, "dada2_taxonomy": {"name": "Silva version 138", "path": "silva_138.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_138"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "silva_138", + "name": "Silva version 138", + "path": "silva_138.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + , "dada2_species": [ + { + "value": "silva_138", + "name": "Silva version 138", + "path": "silva_138.species" + } ] + } +}
--- a/test-data/silvaeuk132_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/silvaeuk132_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "Silva version 132 Eukaryotic 18S", "path": "silva_euk_18S_132.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_euk_18S_132"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "silva_euk_18S_132", + "name": "Silva version 132 Eukaryotic 18S", + "path": "silva_euk_18S_132.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +}
--- a/test-data/unite8fungi_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/unite8fungi_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "UNITE: General Fasta release 8.0 for Fungi", "path": "unite_8.0_fungi.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "unite_8.0_fungi"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "unite_8.0_fungi", + "name": "UNITE: General Fasta release 8.0 for Fungi", + "path": "unite_8.0_fungi.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +}
--- a/test-data/unite8fungisingletons_json Tue May 21 07:35:56 2024 +0000 +++ b/test-data/unite8fungisingletons_json Sat Nov 22 20:07:44 2025 +0000 @@ -1,1 +1,11 @@ -{"data_tables": {"dada2_taxonomy": {"name": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", "path": "unite_8.0_fungi_singletons.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "unite_8.0_fungi_singletons"}}} \ No newline at end of file +{ + "data_tables":{ + "dada2_taxonomy": [ + { + "value": "unite_8.0_fungi_singletons", + "name": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", + "path": "unite_8.0_fungi_singletons.taxonomy", + "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species" + } ] + } +}