[
    {
        "id": "FROGS_remove_chimera",
        "name": "FROGS remove chimera",
        "article": "10.1093\/bib\/bbab318",
        "website": "http:\/\/frogs.toulouse.inrae.fr\/",
        "git": "https:\/\/github.com\/geraldinepascal\/FROGS",
        "description": "Remove PCR chimera in each sample",
        "version": "4.1.0",
        "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html",
        "multiqc": "generic_iframe",
        "commands": [
            {
                "name": "FROGS_remove_chimera",
                "command": "remove_chimera.py",
                "category": "FROGS",
                "output_dir": "FROGS_remove_chimera",
                "inputs": [
                    {
                        "name": "sequence_file",
                        "type": "fasta_file",
                        "description": "the sequences in fasta format"
                    },
                    {
                        "name": "abundance_biom",
                        "type": "biom",
                        "description": "the abundance file"
                    }
                ],
                "outputs": [
                    {
                        "name": "non_chimera_fasta",
                        "file": "non_chimera_fasta.fasta",
                        "type": "fasta_file",
                        "description": "the non chimera sequences"
                    },
                    {
                        "name": "abundance_file",
                        "file": "abundance_biom.biom",
                        "type": "biom",
                        "description": "the abundance file with affiliation"
                    },
                    {
                        "name": "summary",
                        "file": "chimera_report.html",
                        "type": "html",
                        "description": "summary"
                    }
                ],
                "options": [
                    {
                        "name": "FROGS_remove_chimera_threads",
                        "prefix": "-p",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "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_remove_chimera,\n  name: FROGS remove chimera,\n  article: 10.1093\/bib\/bbab318,\n  website: \"http:\/\/frogs.toulouse.inrae.fr\/\",\n  git: \"https:\/\/github.com\/geraldinepascal\/FROGS\",\n  description: \"Remove PCR chimera in each sample\",\n  version: \"4.1.0\",\n  documentation: \"http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html\",\n  multiqc: \"generic_iframe\",\n  commands:\n    [\n      {\n        name: FROGS_remove_chimera,\n        command: \"remove_chimera.py\",\n        category: \"FROGS\",\n        output_dir: FROGS_remove_chimera,\n        inputs: \n          [\n            { name: sequence_file, type: \"fasta_file\", description: \"the sequences in fasta format\"},\n            { name: abundance_biom, type: \"biom\", description: \"the abundance file\"}\n          ],\n        outputs:\n          [\n            { name: \"non_chimera_fasta\", file: \"non_chimera_fasta.fasta\", type: \"fasta_file\", description: \"the non chimera sequences\"},\n            { name: \"abundance_file\", file: \"abundance_biom.biom\", type: \"biom\", description: \"the abundance file with affiliation\"},\n            { name: \"summary\", file: \"chimera_report.html\", type: \"html\", description: \"summary\"}\n          ],\n        options:\n          [\n            {\n              name: FROGS_remove_chimera_threads,\n              prefix: -p,\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      },\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      # vsearch 2.17.0: [\n      #   \"apt-get install autoconf libz-dev libbz2-dev\", # deja install\u00e9\n      #   \"cd \/opt\/biotools\/\",\n      #   \"wget https:\/\/github.com\/torognes\/vsearch\/archive\/v2.17.0.tar.gz\",\n      #   \"tar xzf v2.17.0.tar.gz\",\n      #   \"cd vsearch-2.17.0\",\n      #   \".\/autogen.sh\",\n      #   \".\/configure\",\n      #   \"make\",\n      #   \"make install\"\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  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"
    }
]