[
    {
        "id": "FROGS_cluster",
        "name": "FROGS cluster",
        "article": "10.1093\/bib\/bbab318",
        "website": "http:\/\/frogs.toulouse.inrae.fr\/",
        "git": "https:\/\/github.com\/geraldinepascal\/FROGS",
        "description": "Single-linkage clustering on sequences",
        "version": "4.1.0",
        "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html",
        "multiqc": "generic_iframe",
        "commands": [
            {
                "name": "FROGS_cluster",
                "command": "clustering.py",
                "category": "FROGS",
                "output_dir": "FROGS_cluster",
                "inputs": [
                    {
                        "name": "sequence_file",
                        "type": "fasta_file",
                        "description": "the sequences in fasta format"
                    },
                    {
                        "name": "count_file",
                        "type": "tsv",
                        "description": "the count by sample for each sequence"
                    }
                ],
                "outputs": [
                    {
                        "name": "cluster_seeds",
                        "file": "seed_sequences.fasta",
                        "type": "fasta_file",
                        "description": "The clusters representative sequences"
                    },
                    {
                        "name": "abundance_file",
                        "file": "clustering_abundance.biom",
                        "type": "biom",
                        "description": "The abundance of each cluster in each sample"
                    },
                    {
                        "name": "cluster_composition",
                        "file": "swarms_composition.tsv",
                        "type": "tsv",
                        "description": "A text file representing the read composition of each cluster"
                    }
                ],
                "options": [
                    {
                        "name": "FROGS_cluster_threads",
                        "prefix": "",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "FROGS_cluster_guidelines_version",
                        "prefix": "",
                        "type": "radio",
                        "choices": [
                            {
                                "FROGS 3.2": 3.2
                            },
                            {
                                "FROGS 3.1": 3.1
                            }
                        ],
                        "value": 3.1,
                        "label": "FROGS guidelines for clustering"
                    }
                ]
            }
        ],
        "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_cluster,\n  name: FROGS cluster,\n  article: 10.1093\/bib\/bbab318,\n  website: \"http:\/\/frogs.toulouse.inrae.fr\/\",\n  git: \"https:\/\/github.com\/geraldinepascal\/FROGS\",\n  description: \"Single-linkage clustering on sequences\",\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_cluster,\n        command: \"clustering.py\",\n        category: \"FROGS\",\n        output_dir: FROGS_cluster,\n        inputs: \n          [\n            { name: sequence_file, type: \"fasta_file\", description: \"the sequences in fasta format\"},\n            { name: count_file, type: \"tsv\", description: \"the count by sample for each sequence\"}\n          ],\n        outputs:\n          [\n            { name: \"cluster_seeds\", file: \"seed_sequences.fasta\", type: \"fasta_file\", description: \"The clusters representative sequences\"},\n            { name: \"abundance_file\", file: \"clustering_abundance.biom\", type: \"biom\", description: \"The abundance of each cluster in each sample\"},\n            { name: \"cluster_composition\", file: \"swarms_composition.tsv\", type: \"tsv\", description: \"A text file representing the read composition of each cluster\"}\n          ],\n        options:\n          [\n            {\n              name: FROGS_cluster_threads,\n              prefix: \"\",\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: FROGS_cluster_guidelines_version,\n              prefix: \"\",\n              type:  \"radio\",\n              choices:\n                [\n                  FROGS 3.2: 3.2,\n                  FROGS 3.1: 3.1,\n                ],\n              value: 3.1,\n              label: \"FROGS guidelines for clustering\",\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      # swarm 3.0.O: [\n      #   \"cd \/opt\/biotools\/\",\n      #   \"wget https:\/\/github.com\/torognes\/swarm\/archive\/v3.0.0.tar.gz\",\n      #   \"tar -vxzf v3.0.0.tar.gz\",\n      #   \"cd swarm-3.0.0\/src\",\n      #   \"make\",\n      #   \"cd ..\",\n      # ],\n      # frog_swarm: [\n      # \" ln -s \/opt\/biotools\/swarm-3.0.0\/bin\/swarm \/opt\/biotools\/FROGS-4.1.0\/libexec\/.\"\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"
    }
]