[
    {
        "id": "muscle",
        "name": "MUSCLE",
        "article": "10.1093\/nar\/gkh340",
        "website": "https:\/\/www.drive5.com\/muscle\/",
        "git": "https:\/\/www.drive5.com\/muscle\/downloads.htm",
        "description": "Multiple sequence alignment",
        "version": "5.1",
        "documentation": "https:\/\/www.drive5.com\/muscle\/manual\/index.html",
        "multiqc": "custom",
        "commands": [
            {
                "name": "muscle",
                "cname": "MUSCLE",
                "command": "muscle",
                "category": "phylogenetics",
                "output_dir": "muscle",
                "inputs": [
                    {
                        "name": "fasta",
                        "type": "contigs",
                        "file": "*.fasta",
                        "description": "fasta file",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "aligned_fasta",
                        "type": "aligned_fasta",
                        "file": "output.afa",
                        "description": "aligned fasta file"
                    }
                ],
                "options": [
                    {
                        "name": "muscle_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to fasta file"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "muscle": [
                "Robert C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, Volume 32, Issue 5, 1 March 2004, Pages 1792-1797, https:\/\/doi.org\/10.1093\/nar\/gkh340"
            ]
        },
        "yaml": "{\n  id: muscle,\n  name: MUSCLE ,\n  article: \"10.1093\/nar\/gkh340\",\n  website: \"https:\/\/www.drive5.com\/muscle\/\",\n  git: \"https:\/\/www.drive5.com\/muscle\/downloads.htm\",\n  description: \"Multiple sequence alignment\",\n  version: \"5.1\",\n  documentation: \"https:\/\/www.drive5.com\/muscle\/manual\/index.html\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: muscle,\n        cname: \"MUSCLE\",\n        command: \"muscle\",\n        category: \"phylogenetics\",\n        output_dir: muscle,\n        inputs: [{ name: fasta, type: \"contigs\", file: \"*.fasta\", description: \"fasta file\", from: \"parameter\"}],\n        outputs: [{ name: aligned_fasta, type: \"aligned_fasta\", file: \"output.afa\", description: \"aligned fasta file\"}],\n        options: [\n          {\n            name: muscle_fasta,\n            type: input_file,\n            value: \"\",\n            label: \"Path to fasta file\",\n          },\n        ],\n      },\n    ],\n  install:\n    {\n    #   muscle: [\n    #     \"cd \/opt\/biotools\/\",\n    #     \"wget https:\/\/www.drive5.com\/muscle\/downloads3.8.31\/muscle3.8.31_i86linux64.tar.gz\",\n    #     \"tar -xvzf muscle3.8.31_i86linux64.tar.gz\",\n    #     \"mv muscle3.8.31_i86linux64 bin\/muscle\",\n    #     \"rm muscle3.8.31_i86linux64.tar.gz\"\n    #   ]\n     },\n  citations:\n    {\n      muscle: [\n        \"Robert C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, Volume 32, Issue 5, 1 March 2004, Pages 1792-1797, https:\/\/doi.org\/10.1093\/nar\/gkh340\"\n      ]\n    },\n}\n"
    }
]