[
    {
        "id": "phylip2fasta",
        "name": "phylip to fasta",
        "article": "",
        "website": "",
        "git": "",
        "description": "Conversion of a phylip file to an aligned fasta",
        "version": "1.81",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "phylip2fasta",
                "command": "",
                "category": "format_conversion",
                "output_dir": "phylip2fasta",
                "inputs": [
                    {
                        "name": "phylip",
                        "type": "phylip",
                        "description": "phylip file",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "fasta",
                        "type": "aligned_fasta",
                        "file": "*.fasta",
                        "description": "aligned fasta file"
                    }
                ],
                "options": [
                    {
                        "name": "phylip2fasta_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to phylip file"
                    }
                ]
            }
        ],
        "script": "phylip2fasta.script.py",
        "install": [],
        "citations": {
            "biopython": [
                "Peter J. A. Cock and others, Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, Volume 25, Issue 11, June 2009, Pages 1422\u20131423, https:\/\/doi.org\/10.1093\/bioinformatics\/btp163"
            ]
        },
        "yaml": "{\n  id: phylip2fasta,\n  name: phylip to fasta ,\n  article: \"\",\n  website: \"\",\n  git: \"\",\n  description: \"Conversion of a phylip file to an aligned fasta\",\n  version: \"1.81\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: phylip2fasta,\n        command: \"\",\n        category: \"format_conversion\",\n        output_dir: phylip2fasta,\n        inputs: [{ name: phylip, type: \"phylip\", description: \"phylip file\", from: \"parameter\" } ],\n        outputs: [{ name: fasta, type: \"aligned_fasta\", file: \"*.fasta\", description: \"aligned fasta file\"}],\n        options: [\n          {\n            name: phylip2fasta_fasta,\n            type: input_file,\n            value: \"\",\n            label: \"Path to phylip file\",\n          },\n        ],\n      },\n    ],\n  script: \"phylip2fasta.script.py\",\n  install:\n    {\n      # biopython: [\n      #   \"pip3 install biopython==1.76\"\n      # ]\n    },\n  citations:\n    {\n      biopython: [\n        \"Peter J. A. Cock and others, Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, Volume 25, Issue 11, June 2009, Pages 1422\u20131423, https:\/\/doi.org\/10.1093\/bioinformatics\/btp163\"\n        ],\n    },\n}\n"
    }
]