[ { "id": "dada2_assign_taxonomy", "name": "dada2_assign_taxonomy", "article": "10.1038\/nmeth.3869", "website": "https:\/\/benjjneb.github.io\/dada2", "git": "https:\/\/github.com\/benjjneb\/dada2", "description": "Fast and accurate sample inference from amplicon data with single-nucleotide resolution", "version": "1.26", "documentation": "https:\/\/benjjneb.github.io\/dada2", "multiqc": "krona_iframe", "commands": [ { "name": "dada2_assign_taxonomy", "command": null, "category": "metabarcoding", "output_dir": "dada2_assign_taxonomy", "inputs": [ { "name": "seqs", "type": "fasta_file" }, { "name": "abundance", "type": "tsv", "description": "per sample OTU abundance " } ], "outputs": [ { "name": "taxa_bootstrap", "type": "tsv", "file": "Taxa_bootstrap_mqc.tsv", "description": "Bootstap support table" }, { "name": "taxa_assigment", "type": "tsv", "file": "taxassign.tsv", "description": "Matrix with each row corresponding to an input sequence, and each column corresponding to a taxonomic level" } ], "options": [ { "name": "dada2_assign_taxonomy_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "dada2_assign_taxonomy_reference_fasta", "type": "select", "choices": [ { "Frogs-BOLD_COI-5P": "\/FROGS_taxonomy\/COI\/BOLD_COI-5P" }, { "Frogs-MIDORI": "\/FROGS_taxonomy\/COI\/MIDORI" }, { "Frogs-DAIRYdb": "\/FROGS_taxonomy\/DAIRYdb" }, { "Frogs-Diat.barcode": "\/FROGS_taxonomy\/Diat.barcode" }, { "Frogs-EZBioCloud": "\/FROGS_taxonomy\/EZBioCloud" }, { "Frogs-MaarjAM": "\/FROGS_taxonomy\/MaarjAM" }, { "Frogs-MiDas": "\/FROGS_taxonomy\/MiDas" }, { "Frogs-PHYMYCO_DB": "\/FROGS_taxonomy\/PHYMYCO_DB" }, { "Frogs-PR2": "\/FROGS_taxonomy\/PR2" }, { "Frogs-rbcL": "\/FROGS_taxonomy\/rbcL" }, { "Frogs-rpoB": "\/FROGS_taxonomy\/rpoB" }, { "Frogs-silva_138.1_16S": "\/FROGS_taxonomy\/SILVA\/16S" }, { "Frogs-silva_138.1_18S": "\/FROGS_taxonomy\/SILVA\/18S" }, { "Frogs-silva_138.1_23S": "\/FROGS_taxonomy\/SILVA\/23S" }, { "Frogs-silva_138.1_28S": "\/FROGS_taxonomy\/SILVA\/28S " }, { "Frogs-silva_138.1_LSU": "\/FROGS_taxonomy\/SILVA\/LSU" }, { "Frogs-silva_138.1_SSU": "\/FROGS_taxonomy\/SILVA\/SSU" }, { "Frogs-Unite": "\/FROGS_taxonomy\/Unite" }, { "gyrB": "\/FROGS_taxonomy\/gyrB" }, { "microgreendb": "\/FROGS_taxonomy\/microgreendb" }, { "rdp16 (16S)": "\/taxonomy\/RDP" } ], "value": "\/FROGS_taxonomy\/SILVA\/16S", "label": "Taxonomy source (imported from FROGS http:\/\/genoweb.toulouse.inra.fr\/frogs_databanks\/assignation\/readme.txt" }, { "name": "dada2_assign_taxonomy_tryRC", "prefix": null, "type": "checkbox", "value": false, "label": "try the reverse-complement orientation" }, { "name": "dada2_assign_taxonomy_minBoot", "type": "numeric", "value": 50, "min": 10, "max": 100, "step": 1, "label": "The minimum bootstrap confidence for assigning a taxonomic level." } ] } ], "script": "dada2_assign_taxonomy.script.R", "install": [], "data": [ { "name": "FROGS_taxonomy", "type": "directory" }, { "name": "taxonomy", "type": "directory" } ], "citations": { "dada2": [ "Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038\/nmeth.3869" ], "phyloseq": [ "McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217" ], "biomformat": [ "Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, Volume 1, Issue 1, December 2012, 2047-217X-1-7, https:\/\/doi.org\/10.1186\/2047-217X-1-7" ], "krona": [ "Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385" ], "frogs": [ "Maria Bernard, Olivier Ru\u00e9, Mahendra Mariadassou and G\u00e9raldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093\/bib\/bbab318 " ] }, "yaml": "{\n id: dada2_assign_taxonomy,\n name: dada2_assign_taxonomy,\n article: 10.1038\/nmeth.3869,\n website: \"https:\/\/benjjneb.github.io\/dada2\",\n git: \"https:\/\/github.com\/benjjneb\/dada2\",\n description: \"Fast and accurate sample inference from amplicon data with single-nucleotide resolution\",\n version: \"1.26\",\n documentation: \"https:\/\/benjjneb.github.io\/dada2\",\n multiqc: \"krona_iframe\",\n commands:\n [\n {\n name: dada2_assign_taxonomy,\n command: ~,\n category: \"metabarcoding\",\n output_dir: dada2_assign_taxonomy,\n inputs: [{ name: seqs, type: \"fasta_file\" },\n { name: abundance, type: \"tsv\", description: \"per sample OTU abundance \"} #not mandatory !\n ],\n outputs: [ \n { name: taxa_bootstrap, type: \"tsv\", file: \"Taxa_bootstrap_mqc.tsv\", description: \"Bootstap support table\" },\n { name: taxa_assigment, type: \"tsv\", file: \"taxassign.tsv\", description: \"Matrix with each row corresponding to an input sequence, and each column corresponding to a taxonomic level\" },\n # { name: richness, type: \"png\", file: \"Richness_mqc.png\", description: \"Richness plot\" },\n # { name: top20, type: \"png\", file: \"Top_20_mqc.png\", description: \"Top 20 OTU\" },\n # { name: ps_out, type: \"rds\", file: \"ps_out.rds\", description: \"Phyloseq object\" },\n # { name: ordination, type: \"png\", file: \"Ordination_mqc.png\", description: \"Ordination plot\" },\n # { name: tax_table_biom, type: \"txt\", file: \"tax_table.qiime.txt\", description: \"Taxa table for qiime\" },\n # { name: out_table_biom, type: \"biom\", file: \"otu_table.qiime.biom\", description: \"OTU table for qiime\" },\n ],\n options:\n [\n {\n name: dada2_assign_taxonomy_threads,\n prefix: -t,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: dada2_assign_taxonomy_reference_fasta,\n type: select,\n choices: [\n Frogs-BOLD_COI-5P: \"\/FROGS_taxonomy\/COI\/BOLD_COI-5P\",\n Frogs-MIDORI: \"\/FROGS_taxonomy\/COI\/MIDORI\",\n Frogs-DAIRYdb: \"\/FROGS_taxonomy\/DAIRYdb\",\n Frogs-Diat.barcode: \"\/FROGS_taxonomy\/Diat.barcode\",\n Frogs-EZBioCloud: \"\/FROGS_taxonomy\/EZBioCloud\",\n Frogs-MaarjAM: \"\/FROGS_taxonomy\/MaarjAM\",\n Frogs-MiDas: \"\/FROGS_taxonomy\/MiDas\",\n Frogs-PHYMYCO_DB: \"\/FROGS_taxonomy\/PHYMYCO_DB\",\n Frogs-PR2: \"\/FROGS_taxonomy\/PR2\",\n Frogs-rbcL: \"\/FROGS_taxonomy\/rbcL\",\n Frogs-rpoB: \"\/FROGS_taxonomy\/rpoB\",\n Frogs-silva_138.1_16S: \"\/FROGS_taxonomy\/SILVA\/16S\",\n Frogs-silva_138.1_18S: \"\/FROGS_taxonomy\/SILVA\/18S\",\n Frogs-silva_138.1_23S: \"\/FROGS_taxonomy\/SILVA\/23S\",\n Frogs-silva_138.1_28S: \"\/FROGS_taxonomy\/SILVA\/28S \",\n Frogs-silva_138.1_LSU: \"\/FROGS_taxonomy\/SILVA\/LSU\",\n Frogs-silva_138.1_SSU: \"\/FROGS_taxonomy\/SILVA\/SSU\",\n Frogs-Unite: \"\/FROGS_taxonomy\/Unite\",\n gyrB: \"\/FROGS_taxonomy\/gyrB\",\n microgreendb: \"\/FROGS_taxonomy\/microgreendb\",\n rdp16 (16S): \"\/taxonomy\/RDP\",\n ],\n value: \"\/FROGS_taxonomy\/SILVA\/16S\",\n label: \"Taxonomy source (imported from FROGS http:\/\/genoweb.toulouse.inra.fr\/frogs_databanks\/assignation\/readme.txt\"\n },\n {\n name: dada2_assign_taxonomy_tryRC,\n prefix: ,\n type: checkbox,\n value: FALSE,\n label: \"try the reverse-complement orientation\",\n },\n {\n name: dada2_assign_taxonomy_minBoot,\n type: numeric,\n value: 50,\n min: 10,\n max: 100,\n step: 1,\n label: \"The minimum bootstrap confidence for assigning a taxonomic level.\",\n },\n\n ],\n },\n ],\n script: dada2_assign_taxonomy.script.R, \n install: {\n # dada2: [\n # \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"benjjneb\/dada2\\\", ref=\\\"v1.18\\\");library(\\\"dada2\\\")'\",\n # ],\n # phyloseq: [\n # \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"joey711\/phyloseq\\\");library(\\\"phyloseq\\\")'\"\n # ],\n # biomformat: [\n # \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"joey711\/biomformat\\\");library(\\\"biomformat\\\")'\"\n # ],\n # yaml: [\n # \"Rscript -e 'install.packages(\\\"yaml\\\");'\"\n # ],\n # krona: [\n # \"cd \/opt\/biotools\",\n # \"git clone https:\/\/github.com\/marbl\/Krona.git\",\n # \"cd Krona\/KronaTools\",\n # \".\/install.pl --prefix \/opt\/biotools\",\n # \"cd \/opt\/biotools\",\n # \"rm -r Krona\/ExcelTemplate\"\n # ],\n # mbb_mqc_plugin:\n # [\n # \"cd \/opt\/biotools\",\n # \"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/mmassaviol\/mbb_mqc_plugin.git\",\n # \"cd mbb_mqc_plugin\",\n # \"python3 setup.py install\"\n # ]\n },\n data: [\n {\n name: FROGS_taxonomy,\n type: directory\n },\n {\n name: taxonomy,\n type: directory\n }\n ],\n citations: {\n dada2: [\n \"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038\/nmeth.3869\"\n ],\n phyloseq: [\n \"McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217\"\n ],\n biomformat: [\n \"Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, Volume 1, Issue 1, December 2012, 2047-217X-1-7, https:\/\/doi.org\/10.1186\/2047-217X-1-7\"\n ],\n krona: [\n \"Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385\"\n ],\n frogs: [\n \"Maria Bernard, Olivier Ru\u00e9, Mahendra Mariadassou and G\u00e9raldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093\/bib\/bbab318 \"\n ]\n\n }\n}\n" } ]