[
    {
        "id": "quast",
        "name": "QUAST",
        "article": "10.1093\/bioinformatics\/btt086",
        "website": "http:\/\/bioinf.spbau.ru\/quast",
        "git": "https:\/\/github.com\/ablab\/quast",
        "description": "Quality Assessment Tool for Genome Assemblies",
        "version": "5.2.0",
        "documentation": "http:\/\/quast.bioinf.spbau.ru\/manual.html",
        "multiqc": "quast",
        "commands": [
            {
                "name": "quast",
                "command": "quast.py",
                "category": "quality",
                "output_dir": "quast",
                "inputs": [
                    {
                        "name": "assembly",
                        "type": "contigs"
                    }
                ],
                "outputs": [
                    {
                        "name": "report",
                        "type": "tsv",
                        "file": "report.tsv",
                        "description": "Report (tabulated file)"
                    }
                ],
                "options": [
                    {
                        "name": "quast_threads",
                        "prefix": "--threads",
                        "value": 4,
                        "min": 1,
                        "max": 32,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "quast": [
                "Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8, 15 April 2013, Pages 1072-1075, https:\/\/doi.org\/10.1093\/bioinformatics\/btt086"
            ]
        },
        "yaml": "{\n  id: quast,\n  name: QUAST,\n  article: 10.1093\/bioinformatics\/btt086,\n  website: \"http:\/\/bioinf.spbau.ru\/quast\",\n  git: \"https:\/\/github.com\/ablab\/quast\",\n  description: \"Quality Assessment Tool for Genome Assemblies\",\n  version: \"5.2.0\",\n  documentation: \"http:\/\/quast.bioinf.spbau.ru\/manual.html\",\n  multiqc: \"quast\",\n  commands:\n    [\n      {\n        name: quast,\n        command: quast.py,\n        category: \"quality\",\n        output_dir: quast,\n        inputs: [{ name: assembly, type: \"contigs\" }],\n        outputs:\n          [\n            { name: report, type: \"tsv\", file: \"report.tsv\", description: \"Report (tabulated file)\" }\n          ],\n        options:\n          [\n            {\n              name: \"quast_threads\",\n              prefix: \"--threads\",\n              value: 4,\n              min: 1,\n              max: 32,\n              step: 1,\n              label: \"Threads to use\",\n              type: \"numeric\",\n            },\n          ],\n      },\n    ],\n  install:\n    {\n      # quast_apt_dependencies: [\n      #   \"apt-get update\",\n      #   \"apt-get install -y zlib1g-dev pkg-config libfreetype6-dev libpng-dev python-matplotlib python-setuptools\"\n      # ],\n      # quast: [\n      #   \"cd \/opt\/biotools\",\n      #   \"git clone https:\/\/github.com\/ablab\/quast.git\",\n      #   \"cd quast\",\n      #   \"python3 .\/setup.py install_full\",\n      #   \"cd .. && rm -rf quast*\"\n      # ]\n    },\n    citations:  {\n      quast: [\n        \"Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8, 15 April 2013, Pages 1072-1075, https:\/\/doi.org\/10.1093\/bioinformatics\/btt086\"\n      ]\n    }\n}\n"
    }
]