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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dada2 commit dd3f70e1c8020928bc271e491045a36ffcc7fe5c
author iuc
date Fri, 12 Dec 2025 09:06:55 +0000
parents cd817c959692
children
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7:cd817c959692 8:b84aace42ca8
1 <tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.2" profile="24.2"> 1 <tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.3" profile="24.2">
2 <description>Download reference databases</description> 2 <description>Download reference databases</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.25.0">wget</requirement> 4 <requirement type="package" version="1.25.0">wget</requirement>
5 <requirement type="package" version="6.0">unzip</requirement> 5 <requirement type="package" version="6.0">unzip</requirement>
6 </requirements> 6 </requirements>
21 "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", 21 "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
22 "rdp_19_toGenus": "https://zenodo.org/records/14168771/files/rdp_19_toGenus_trainset.fa.gz?download=1", 22 "rdp_19_toGenus": "https://zenodo.org/records/14168771/files/rdp_19_toGenus_trainset.fa.gz?download=1",
23 "rdp_19_toSpecies": "https://zenodo.org/records/14168771/files/rdp_19_toSpecies_trainset.fa.gz?download=1", 23 "rdp_19_toSpecies": "https://zenodo.org/records/14168771/files/rdp_19_toSpecies_trainset.fa.gz?download=1",
24 "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", 24 "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
25 "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1", 25 "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
26 "unite_10.0_eukaryotes-2025-02-19": "https://s3.hpc.ut.ee/plutof-public/original/e861a3d6-54f4-42dc-882a-5f129beac39a.tgz",
27 "unite_10.0_eukaryotes_singletons-2025-02-19": "https://s3.hpc.ut.ee/plutof-public/original/b02db549-5f04-43fc-afb6-02888b594d10.tgz",
26 "unite_8.0_fungi": "https://s3.hpc.ut.ee/plutof-public/original/9f7b41c3-825b-4db8-9c52-74a4603a860a.zip", 28 "unite_8.0_fungi": "https://s3.hpc.ut.ee/plutof-public/original/9f7b41c3-825b-4db8-9c52-74a4603a860a.zip",
27 "unite_8.0_fungi_singletons": "https://s3.hpc.ut.ee/plutof-public/original/53dfc9ce-9cb5-4205-84bb-f47faff26462.zip", 29 "unite_8.0_fungi_singletons": "https://s3.hpc.ut.ee/plutof-public/original/53dfc9ce-9cb5-4205-84bb-f47faff26462.zip",
28 "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1", 30 "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
29 "greengenes2_2024.09_toGenus": "https://zenodo.org/records/14169078/files/gg2_2024_09_toGenus_trainset.fa.gz?download=1", 31 "greengenes2_2024.09_toGenus": "https://zenodo.org/records/14169078/files/gg2_2024_09_toGenus_trainset.fa.gz?download=1",
30 "greengenes2_2024.09_toSpecies": "https://zenodo.org/records/14169078/files/gg2_2024_09_toSpecies_trainset.fa.gz?download=1", 32 "greengenes2_2024.09_toSpecies": "https://zenodo.org/records/14169078/files/gg2_2024_09_toSpecies_trainset.fa.gz?download=1",
53 } 55 }
54 mkdir -p '${out_file.extra_files_path}' && 56 mkdir -p '${out_file.extra_files_path}' &&
55 cd '${out_file.extra_files_path}' && 57 cd '${out_file.extra_files_path}' &&
56 #for $database in $taxonomy_databases: 58 #for $database in $taxonomy_databases:
57 wget '$FILE2TAXURL[str($database)]' -O '${database}.taxonomy' && 59 wget '$FILE2TAXURL[str($database)]' -O '${database}.taxonomy' &&
58 #if str($database).startswith("unite") 60 #if str($database).startswith("unite_8.0")
59 unzip -p '${database}.taxonomy' "*.fasta" -x "developer/*" > tmp && 61 unzip -p '${database}.taxonomy' "*.fasta" -x "developer/*" > tmp &&
60 mv tmp '${database}.taxonomy' && 62 mv tmp '${database}.taxonomy' &&
61 #end if 63 #end if
62 #end for 64 #end for
63 #if $species_databases 65 #if $species_databases
91 "rdp_16": "RDP trainset 16", 93 "rdp_16": "RDP trainset 16",
92 "rdp_14": "RDP trainset 14", 94 "rdp_14": "RDP trainset 14",
93 "greengenes_13.84": "GreenGenes version 13.84", 95 "greengenes_13.84": "GreenGenes version 13.84",
94 "greengenes2_2024.09_toGenus": "GreenGenes2 release 2024.09 to Genus (for short reads)", 96 "greengenes2_2024.09_toGenus": "GreenGenes2 release 2024.09 to Genus (for short reads)",
95 "greengenes2_2024.09_toSpecies": "GreenGenes2 release 2024.09 to Species (for long reads)", 97 "greengenes2_2024.09_toSpecies": "GreenGenes2 release 2024.09 to Species (for long reads)",
98 "unite_10.0_eukaryotes-2025-02-19": "UNITE: General Fasta release 10.0 (2025-02-19) for Eukaroyes",
99 "unite_10.0_eukaryotes_singletons-2025-02-19": "UNITE: General Fasta release 10.0 (2025-02-19) for Eukaroyes including global and 97% singletons",
96 "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi", 100 "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi",
97 "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", 101 "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons",
98 "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", 102 "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)",
99 103
100 "gtdb_202_toGenus": "GTDB Version 202 to Genus (for short reads)", 104 "gtdb_202_toGenus": "GTDB Version 202 to Genus (for short reads)",
162 <option value="rdp_16">RDP 16</option> 166 <option value="rdp_16">RDP 16</option>
163 <option value="rdp_14">RDP 14</option> 167 <option value="rdp_14">RDP 14</option>
164 <option value="greengenes2_2024.09_toGenus">GreenGenes2 2024.09 to Genus (for short reads)</option> 168 <option value="greengenes2_2024.09_toGenus">GreenGenes2 2024.09 to Genus (for short reads)</option>
165 <option value="greengenes2_2024.09_toSpecies">GreenGenes2 2024.09 to Species (for long reads)</option> 169 <option value="greengenes2_2024.09_toSpecies">GreenGenes2 2024.09 to Species (for long reads)</option>
166 <option value="greengenes_13.84">GreenGenes 13.84</option> 170 <option value="greengenes_13.84">GreenGenes 13.84</option>
167 <option value="unite_8.0_fungi">UNITE Fungi: General Fasta 8.0 for Fungi</option> 171 <option value="unite_10.0_eukaryotes-2025-02-19">UNITE General Fasta 10.0 (2025-02-19) for Eukaryota</option>
168 <option value="unite_8.0_fungi_singletons">UNITE Fungi: General Fasta release 8.0 for Fungi including global and 97% singletons</option> 172 <option value="unite_10.0_eukaryotes_singletons-2025-02-19">UNITE: General Fasta release 10.0 (2025-02-19) for Eukaryota including global and 97% singletons</option>
173 <option value="unite_8.0_fungi">UNITE: General Fasta 8.0 for Fungi</option>
174 <option value="unite_8.0_fungi_singletons">UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons</option>
169 <!-- UNITE Eukaryotes not yet supported https://github.com/benjjneb/dada2/issues/702 --> 175 <!-- UNITE Eukaryotes not yet supported https://github.com/benjjneb/dada2/issues/702 -->
170 <option value="RefSeq_RDP_2018_05">NCBI RefSeq 16S rRNA database supplemented by RDP 05/2018</option> 176 <option value="RefSeq_RDP_2018_05">NCBI RefSeq 16S rRNA database supplemented by RDP 05/2018</option>
171 <option value="gtdb_202_toGenus">GTDB: Genome Taxonomy Database 202 to Genus (for short reads) </option> 177 <option value="gtdb_202_toGenus">GTDB: Genome Taxonomy Database 202 to Genus (for short reads) </option>
172 <option value="gtdb_202_toSpecies">GTDB: Genome Taxonomy Database 202 to Species (for long reads) </option> 178 <option value="gtdb_202_toSpecies">GTDB: Genome Taxonomy Database 202 to Species (for long reads) </option>
173 <option value="gtdb_2018_11">GTDB: Genome Taxonomy Database 11/2018</option> 179 <option value="gtdb_2018_11">GTDB: Genome Taxonomy Database 11/2018</option>
290 <assert_command> 296 <assert_command>
291 <has_text text="wget" n="1"/> 297 <has_text text="wget" n="1"/>
292 </assert_command> 298 </assert_command>
293 </test> 299 </test>
294 <test> 300 <test>
301 <param name="taxonomy_databases" value="unite_10.0_eukaryotes-2025-02-19"/>
302 <output name="out_file">
303 <assert_contents>
304 <has_text text='"value": "unite_10.0_eukaryotes-2025-02-19"'/>
305 </assert_contents>
306 </output>
307 <assert_command>
308 <has_text text="wget" n="1"/>
309 <has_text text="unzip" negate="true"/>
310 </assert_command>
311 </test>
312 <test>
313 <param name="taxonomy_databases" value="unite_10.0_eukaryotes_singletons-2025-02-19"/>
314 <output name="out_file">
315 <assert_contents>
316 <has_text text='"value": "unite_10.0_eukaryotes_singletons-2025-02-19"'/>
317 </assert_contents>
318 </output>
319 <assert_command>
320 <has_text text="wget" n="1"/>
321 </assert_command>
322 </test>
323
324 <test>
295 <param name="taxonomy_databases" value="unite_8.0_fungi"/> 325 <param name="taxonomy_databases" value="unite_8.0_fungi"/>
296 <output name="out_file" file="unite8fungi_json"/> 326 <output name="out_file" file="unite8fungi_json"/>
297 <assert_command> 327 <assert_command>
298 <has_text text="unzip"/> 328 <has_text text="unzip"/>
299 </assert_command> 329 </assert_command>