[
    {
        "id": "abricate",
        "name": "ABRicate",
        "description": "Mass screening of contigs for antimicrobial resistance or virulence genes",
        "version": "1.0.1",
        "website": "https:\/\/github.com\/tseemann\/abricate\/tree\/v1.0.1",
        "git": "https:\/\/github.com\/tseemann\/abricate\/tree\/v1.0.1",
        "documentation": "https:\/\/github.com\/tseemann\/abricate\/blob\/v1.0.1\/README.md",
        "article": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "abricate",
                "output_dir": "abricate",
                "category": "metagenomic",
                "command": "abricate",
                "inputs": [
                    {
                        "name": "contigs",
                        "file": "",
                        "type": "contigs",
                        "description": "Contigs in fasta format"
                    }
                ],
                "outputs": [
                    {
                        "name": "output",
                        "file": "output.tsv",
                        "type": "tsv",
                        "description": "Output table"
                    }
                ],
                "options": [
                    {
                        "name": "abricate_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "abricate_database",
                        "prefix": "--db",
                        "type": "select",
                        "choices": [
                            {
                                "card": "card"
                            },
                            {
                                "resfinder": "resfinder"
                            },
                            {
                                "megares": "megares"
                            },
                            {
                                "argannot": "argannot"
                            },
                            {
                                "ecoli_vf": "ecoli_vf"
                            },
                            {
                                "plasmidfinder": "plasmidfinder"
                            },
                            {
                                "vfdb": "vfdb"
                            },
                            {
                                "ncbi": "ncbi"
                            }
                        ],
                        "value": "ncbi",
                        "label": "Database to use"
                    },
                    {
                        "name": "abricate_minid",
                        "prefix": "--minid",
                        "type": "numeric",
                        "value": 80,
                        "min": 0,
                        "max": 100,
                        "step": 0.1,
                        "label": "Minimum DNA %identity"
                    },
                    {
                        "name": "abricate_mincov",
                        "prefix": "--mincov",
                        "type": "numeric",
                        "value": 80,
                        "min": 0,
                        "max": 100,
                        "step": 0.1,
                        "label": "Minimum DNA %coverage"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "abricate": [
                "Seemann T, Abricate, Github https:\/\/github.com\/tseemann\/abricate"
            ]
        },
        "yaml": "{\n  id: \"abricate\",\n  name: \"ABRicate\",\n  description: \"Mass screening of contigs for antimicrobial resistance or virulence genes\",\n  version: \"1.0.1\",\n  website: \"https:\/\/github.com\/tseemann\/abricate\/tree\/v1.0.1\",\n  git: \"https:\/\/github.com\/tseemann\/abricate\/tree\/v1.0.1\",\n  documentation: \"https:\/\/github.com\/tseemann\/abricate\/blob\/v1.0.1\/README.md\",\n  article: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: \"abricate\",\n        output_dir: \"abricate\",\n        category: \"metagenomic\",\n        command: \"abricate\",\n        inputs:\n          [\n            {\n              name: \"contigs\",\n              file: \"\",\n              type: \"contigs\",\n              description: \"Contigs in fasta format\",\n            },\n          ],\n        outputs:\n          [{ name: \"output\", file: \"output.tsv\", type: \"tsv\", description: \"Output table\" }],\n        options:\n          [\n            {\n              name: \"abricate_threads\",\n              prefix: \"--threads\",\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: \"abricate_database\",\n              prefix: \"--db\",\n              type: \"select\",\n              choices:\n                [\n                  card: \"card\",\n                  resfinder: \"resfinder\",\n                  megares: \"megares\",\n                  argannot: \"argannot\",\n                  ecoli_vf: \"ecoli_vf\",\n                  plasmidfinder: \"plasmidfinder\",\n                  vfdb: \"vfdb\",\n                  ncbi: \"ncbi\",\n                ],\n              value: \"ncbi\",\n              label: \"Database to use\",\n            },\n            {\n              name: \"abricate_minid\",\n              prefix: \"--minid\",\n              type: \"numeric\",\n              value: 80,\n              min: 0,\n              max: 100,\n              step: 0.1,\n              label: \"Minimum DNA %identity\",\n            },\n            {\n              name: \"abricate_mincov\",\n              prefix: \"--mincov\",\n              type: \"numeric\",\n              value: 80,\n              min: 0,\n              max: 100,\n              step: 0.1,\n              label: \"Minimum DNA %coverage\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # any2fasta: [\n    #   \"apt-get update\",\n    #   \"cd \/opt\/biotools\/bin\",\n    #   \"wget https:\/\/raw.githubusercontent.com\/tseemann\/any2fasta\/master\/any2fasta\",\n    #   \"chmod +x any2fasta\"\n    # ],\n    # abricate: [\n    #   \"apt-get install -y bioperl ncbi-blast+ libjson-perl libtext-csv-perl libpath-tiny-perl liblwp-protocol-https-perl libwww-perl\",\n    #   \"cd \/opt\/biotools\",\n    #   \"git clone --depth 1 --branch v1.0.1 https:\/\/github.com\/tseemann\/abricate.git\",\n    #   \".\/abricate\/bin\/abricate --check\",\n    #   \".\/abricate\/bin\/abricate --setupdb\",\n    #   \".\/abricate\/bin\/abricate .\/abricate\/test\/assembly.fa\",\n    #   \"cd bin\",\n    #   \"ln -s \/opt\/biotools\/abricate\/bin\/abricate abricate\"\n    # ]\n  },\n  citations: {\n    abricate: [\"Seemann T, Abricate, Github https:\/\/github.com\/tseemann\/abricate\"]\n  }\n}\n"
    }
]