[
    {
        "id": "FROGS_biom_to_tsv",
        "name": "FROGS biom2tsv",
        "article": "10.1093\/bib\/bbab318",
        "website": "http:\/\/frogs.toulouse.inrae.fr\/",
        "git": "https:\/\/github.com\/geraldinepascal\/FROGS",
        "description": "Adding taxonomic affiliation in abundance file",
        "version": "4.1.0",
        "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html",
        "multiqc": "custom",
        "commands": [
            {
                "name": "FROGS_biom_to_tsv",
                "command": "biom_to_tsv.py",
                "category": "FROGS",
                "output_dir": "FROGS_biom_to_tsv",
                "inputs": [
                    {
                        "name": "biom",
                        "type": "biom",
                        "description": "the abundance of each OTU in each sample"
                    }
                ],
                "outputs": [
                    {
                        "name": "abundance_file",
                        "file": "tax_affiliation.tsv",
                        "type": "tsv",
                        "description": "output file with the abundance and metadata (tsv)"
                    },
                    {
                        "name": "lulu_abundance_file",
                        "file": "simple_OTU_abundance.tsv",
                        "type": "tsv",
                        "description": "OTU abundance with samples as columns and OTUs as rows (for lulu)"
                    }
                ],
                "options": []
            }
        ],
        "install": [],
        "citations": {
            "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: FROGS_biom_to_tsv,\n  name: FROGS biom2tsv,\n  article: 10.1093\/bib\/bbab318,\n  website: \"http:\/\/frogs.toulouse.inrae.fr\/\",\n  git: \"https:\/\/github.com\/geraldinepascal\/FROGS\",\n  description: \"Adding taxonomic affiliation in abundance file\",\n  version: \"4.1.0\",\n  documentation: \"http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: FROGS_biom_to_tsv,\n        command: \"biom_to_tsv.py\",\n        category: \"FROGS\",\n        output_dir: FROGS_biom_to_tsv,\n        inputs: \n          [\n            #{ name: fasta, type: \"fasta_file\", description: \"the sequences in fasta format\"},\n            { name: biom, type: \"biom\", description: \"the abundance of each OTU in each sample\"}\n          ],\n        outputs:\n          [\n            { name: \"abundance_file\", file: \"tax_affiliation.tsv\", type: \"tsv\", description: \"output file with the abundance and metadata (tsv)\"},\n            { name: \"lulu_abundance_file\", file: \"simple_OTU_abundance.tsv\", type: \"tsv\", description: \"OTU abundance with samples as columns and OTUs as rows (for lulu)\"},\n\n          ],\n        options:\n          [\n           \n          ],\n      },\n    ],\n  install:\n    {\n      # perl: [\n      #   \"sudo apt-get install python3 perl\" # deja install\u00e9\n      # ],\n      # frogs: [\n      #   \"cd \/opt\/biotools\",\n      #   \"wget https:\/\/github.com\/geraldinepascal\/FROGS\/archive\/v4.1.0.tar.gz\",\n      #   \"tar -zxvf v4.1.0.tar.gz\",\n      #   \"cd FROGS-4.1.0\",\n      #   \"mkdir bin\"\n      # ],\n      # scipy: [\n      #   \"apt-get install python3-scipy\" # demande confirmation\n      # ],\n    },\n  citations:  {\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"
    }
]