[
    {
        "id": "dada2_assign_taxonomy_customDB",
        "name": "dada2_assign_taxonomy_customDB",
        "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_customDB",
                "command": null,
                "category": "metabarcoding",
                "output_dir": "dada2_assign_taxonomy_customDB",
                "inputs": [
                    {
                        "name": "seqs",
                        "type": "fasta_file"
                    },
                    {
                        "name": "abundance",
                        "type": "tsv",
                        "description": "per sample OTU abundance "
                    },
                    {
                        "name": "FROGS_fasta_db",
                        "type": "fasta_file",
                        "description": "fasta file with sames seqID as FROGS_tax_db"
                    },
                    {
                        "name": "FROGS_tax_db",
                        "type": "taxonomyDB",
                        "description": "tabulate file : 'SeqID\tKingdom;Phylum;Class;Order;Family;Genus;Species'. All taxonomies need to be define with the exact same number of rank separate by ';'. Set 'unclassified' for unknown rank"
                    }
                ],
                "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_customDB_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "dada2_assign_taxonomy_customDB_tryRC",
                        "prefix": null,
                        "type": "checkbox",
                        "value": false,
                        "label": "try the reverse-complement orientation"
                    },
                    {
                        "name": "dada2_assign_taxonomy_customDB_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_customDB.script.R",
        "install": [],
        "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_customDB,\n  name: dada2_assign_taxonomy_customDB,\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_customDB,\n        command: ~,\n        category: \"metabarcoding\",\n        output_dir: dada2_assign_taxonomy_customDB,\n        inputs: [\n          { name: seqs, type: \"fasta_file\" },\n          { name: abundance, type: \"tsv\", description: \"per sample OTU abundance \"}, #not mandatory !\n          { name: FROGS_fasta_db, type: \"fasta_file\", description: \"fasta file with sames seqID as FROGS_tax_db\"},\n          { name: FROGS_tax_db, type: \"taxonomyDB\", description: \"tabulate file : 'SeqID\\tKingdom;Phylum;Class;Order;Family;Genus;Species'. All taxonomies need to be define with the exact same number of rank separate by ';'. Set 'unclassified' for unknown rank\"}\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_customDB_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_customDB_tryRC,\n              prefix: ,\n              type: checkbox,\n              value: FALSE,\n              label: \"try the reverse-complement orientation\",\n            },\n            {\n              name: dada2_assign_taxonomy_customDB_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_customDB.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"
    }
]