[
    {
        "id": "metabat1",
        "name": "MetaBAT1",
        "description": "Metagenome Binning based on Abundance and Tetranucleotide frequency",
        "version": "1.2.15",
        "website": "https:\/\/bitbucket.org\/berkeleylab\/metabat",
        "git": "https:\/\/bitbucket.org\/berkeleylab\/metabat",
        "documentation": "https:\/\/bitbucket.org\/berkeleylab\/metabat\/wiki\/Home",
        "article": "10.7717\/peerj.1165",
        "multiqc": "custom",
        "commands": [
            {
                "name": "metabat1",
                "output_dir": "metabat1",
                "category": "metagenomic",
                "command": "metabat1",
                "inputs": [
                    {
                        "name": "contigs",
                        "file": "",
                        "type": "contigs",
                        "description": "Contigs in fasta format"
                    }
                ],
                "outputs": [
                    {
                        "name": "fasta_bins",
                        "file": "{bin.fasta}",
                        "type": "fasta",
                        "description": "Bins in fasta format"
                    }
                ],
                "options": [
                    {
                        "name": "metabat1_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "metabat1_mincontig",
                        "prefix": "--minContig",
                        "type": "numeric",
                        "value": 2500,
                        "min": 1500,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum size of a contig for binning"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "metabat": [
                "Kang DD, Froula J, Egan R, Wang Z. 2015. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165 https:\/\/doi.org\/10.7717\/peerj.1165"
            ]
        },
        "yaml": "{\n  id: \"metabat1\",\n  name: \"MetaBAT1\",\n  description: \"Metagenome Binning based on Abundance and Tetranucleotide frequency\",\n  version: \"1.2.15\",\n  website: \"https:\/\/bitbucket.org\/berkeleylab\/metabat\",\n  git: \"https:\/\/bitbucket.org\/berkeleylab\/metabat\",\n  documentation: \"https:\/\/bitbucket.org\/berkeleylab\/metabat\/wiki\/Home\",\n  article: \"10.7717\/peerj.1165\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: \"metabat1\",\n        output_dir: \"metabat1\",\n        category: \"metagenomic\",\n        command: \"metabat1\",\n        inputs:\n          [\n            {\n              name: \"contigs\",\n              file: \"\",\n              type: \"contigs\",\n              description: \"Contigs in fasta format\",\n            },\n          ],\n        outputs:\n          [\n            {\n              name: \"fasta_bins\",\n              file: \"{bin.fasta}\",\n              type: \"fasta\",\n              description: \"Bins in fasta format\",\n            },\n          ],\n        options:\n          [\n            {\n              name: \"metabat1_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: \"metabat1_mincontig\",\n              prefix: \"--minContig\",\n              type: \"numeric\",\n              value: 2500,\n              min: 1500,\n              max: NA,\n              step: 1,\n              label: \"Minimum size of a contig for binning\",\n            },\n          ],\n      },\n    ],\n  install:\n    {\n      # metabat:\n      #   [\n      #     \"cd \/opt\/biotools\",\n      #     \"wget https:\/\/bitbucket.org\/berkeleylab\/metabat\/downloads\/metabat-static-binary-linux-x64_v2.12.1.tar.gz\",\n      #     \"tar -xvzf metabat-static-binary-linux-x64_v2.12.1.tar.gz\",\n      #     \"rm metabat-static-binary-linux-x64_v2.12.1.tar.gz\",\n      #     \"cd bin\",\n      #     \"ln -s \/opt\/biotools\/metabat\/metabat metabat\",\n      #   ],\n    },\n  citations:\n    {\n      metabat:\n        [\n          \"Kang DD, Froula J, Egan R, Wang Z. 2015. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165 https:\/\/doi.org\/10.7717\/peerj.1165\",\n        ],\n    },\n}\n"
    }
]