data_manager_dada2: data_manager/dada2

annotate data_manager/dada2_fetcher.xml @ 7:cd817c959692 draft

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 20:07:31 +0000
parents	2e7c3f0f2c6d
children	b84aace42ca8

rev	line source
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	1 <tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.2" 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",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	26 "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	27 "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	28 "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	29 "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	30 "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	31 "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	32
cd817c959692 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 "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	34 "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	35 "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	36
cd817c959692 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 "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	38 "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	39 "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	40 }
cd817c959692 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 ## 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	42 #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	43 "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	44 "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	45 "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	46 "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	47 "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	48 "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	49 "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	50 "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	51 "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	52 "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	53 }
cd817c959692 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 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	55 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	56 #for $database in $taxonomy_databases:
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	57 wget '$FILE2TAXURL[str($database)]' -O '${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	58 #if str($database).startswith("unite")
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	59 unzip -p '${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	60 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	61 #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	62 #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	63 #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	64 #for $database in $species_databases:
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	65 wget '$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	66 #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	67 #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	68 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	69 ]]>
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	70 </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	71 <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	72 <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	73 #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	74 "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	75 "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	76 "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	77
cd817c959692 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_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	79 "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	80 "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	81
cd817c959692 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_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	83 "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	84 "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	85
cd817c959692 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": "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	87 "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	88 "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	89 "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	90 "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	91 "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	92 "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	93 "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	94 "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	95 "greengenes2_2024.09_toSpecies": "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	96 "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	97 "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	98 "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	99
cd817c959692 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 "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	101 "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	102 "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	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_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	105 "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	106 "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	107 "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	108 }
cd817c959692 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 #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	110 "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	111 }
cd817c959692 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 "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	114 "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	115 #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	116 #set taxlevels = FILE2TAXLEVELS.get(str($database), "Kingdom,Phylum,Class,Order,Family,Genus,Species")
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	117 {
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	118 "value": "$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	119 "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	120 "path": "${database}.taxonomy",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	121 "taxlevels": "$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	122 }#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	123 #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	124 ,
cd817c959692 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 #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	126 #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	127 ]
cd817c959692 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 #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	129 , "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	130 #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	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 "value": "$database",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	133 "name": "$FILE2NAME[str($database)]",
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	134 "path": "${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	135 }#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	136 #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	137 ,
cd817c959692 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 #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	139 #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	140 ]
cd817c959692 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 #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	142 }
cd817c959692 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 }
cd817c959692 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 ]]></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	145 </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	146 <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	147 <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	148 <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	149 <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	150
cd817c959692 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 <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	152 <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	153
cd817c959692 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 <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	155 <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	156
cd817c959692 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 <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	158 <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	159 <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	160 <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	161 <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	162 <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	163 <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	164 <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	165 <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	166 <option value="greengenes_13.84">GreenGenes 13.84</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="unite_8.0_fungi">UNITE Fungi: General Fasta 8.0 for Fungi</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="unite_8.0_fungi_singletons">UNITE Fungi: General Fasta release 8.0 for Fungi including global and 97% singletons</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 <!-- 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	170 <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	171 <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	172 <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	173 <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	174 <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	175 <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	176 <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	177 </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	178 <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	179 <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	180 <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	181 <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	182 <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	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 </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	190 </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	191 <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	192 <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	193 </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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <has_text text=""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	201 <has_text text=""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	202 <has_text text=""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	203 </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	204 </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	205 <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	206 <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	207 </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	208 </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	209
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	210 <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	211 <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	212 <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	213 <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	214 <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	215 <has_text text=""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	216 <has_text text=""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	217 <has_text text=""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	218 </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	219 </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	220 <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	221 <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	222 </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	223 </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	224 <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	225 <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	226 <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	227 <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	228 <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	229 <has_text text=""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	230 <has_text text=""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	231 <has_text text=""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	232 </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	233 </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	234 <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	235 <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	236 </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	237 </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	238
cd817c959692 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 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 </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	246 </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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 </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	254 </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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 </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	262 </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	263 <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	264 <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	265 </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	266 </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	267 <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	268 <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	269 <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	270 <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	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 <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	273 </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	274 </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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 </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	282 </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	283 <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	284 <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	285 </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	286 </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	287 <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	288 <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	289 <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	290 <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	291 <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	292 </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	293 </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	294 <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	295 <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	296 <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	297 <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	298 <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	299 </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	300 </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	301 <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	302 <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	303 <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	304 <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	305 <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	306 </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	307 </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	308 <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	309 <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	310 <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	311 <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	312 <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	313 </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	314 </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	315
cd817c959692 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit 5f2ed0407e3adaafc6070fc0594a4685ade094db iuc parents: 6 diff changeset	316 <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	317 <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	318 <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	319 <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	320 <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	321 <has_text text=""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	322 <has_text text=""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	323 <has_text text=""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	324 </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	325 </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	326 <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	327 <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	328 </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	329 </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	330
cd817c959692 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="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	333 <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	334 <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	335 <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	336 <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	337 </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	338 </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	339 <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	340 <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	341 <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	342 <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	343 <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	344 </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	345 </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	346 <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	347 <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	348 <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	349 <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	350 <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	351 </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	352 </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	353 <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	354 <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	355 <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	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="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	358 </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	359 </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	360 </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	361 <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	362 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	363 ..........................................................
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
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	365 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	366
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	367 - 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	368 - 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	369 - 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	370 - 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	371 - 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	372
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	373 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	374
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	375 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	376
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	377 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	378
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	379 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	380
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	381 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	382 ..............................................................
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
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	384 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	385
632251c6912c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e" iuc parents: diff changeset	386 - 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	387 - 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	388 - 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	389 - 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	390 - 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	391 - 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	392
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 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	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 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	396 ]]></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	397 <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	398 <!-- 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	399 <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	400 <!-- 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	401 <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	402 <!-- 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	403 <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	404 <!-- 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	405 <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	406 <!-- 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	407 <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	408 <!-- 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	409 <!-- 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	410 <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	411 <!-- 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	412 <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	413 </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	414 </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	415

Mercurial > repos > iuc > data_manager_dada2

annotate data_manager/dada2_fetcher.xml @ 7:cd817c959692 draft