[
    {
        "id": "transdecoder",
        "name": "TransDecoder",
        "article": null,
        "website": "https:\/\/github.com\/TransDecoder\/TransDecoder",
        "git": "https:\/\/github.com\/TransDecoder\/TransDecoder",
        "description": "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.",
        "version": "5.7.1",
        "documentation": "https:\/\/github.com\/TransDecoder\/TransDecoder\/wiki",
        "commands": [
            {
                "name": "transdecoder",
                "cname": "TransDecoder",
                "command": "transdecoder",
                "category": "post_assembly",
                "output_dir": "transdecoder",
                "inputs": [
                    {
                        "name": "assembly_fasta",
                        "type": "contigs",
                        "description": "Assembly fasta"
                    }
                ],
                "outputs": [
                    {
                        "name": "pep",
                        "type": "contigs",
                        "description": "Pep"
                    },
                    {
                        "name": "cds",
                        "type": "contigs",
                        "description": "Cds"
                    },
                    {
                        "name": "gff3",
                        "type": "gff3",
                        "description": "Gff3"
                    },
                    {
                        "name": "bed",
                        "type": "bed",
                        "description": "Bed"
                    }
                ],
                "options": [
                    {
                        "name": "transdecoder_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "transdecoder": [
                "Haas, BJ. https:\/\/github.com\/TransDecoder\/TransDecoder"
            ]
        },
        "yaml": "{\n  id: transdecoder,\n  name: TransDecoder,\n  article: ~,\n  website: \"https:\/\/github.com\/TransDecoder\/TransDecoder\",\n  git: \"https:\/\/github.com\/TransDecoder\/TransDecoder\",\n  description: \"TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.\",\n  version: \"5.7.1\",\n  documentation: \"https:\/\/github.com\/TransDecoder\/TransDecoder\/wiki\",\n  commands:\n    [\n      {\n        name: transdecoder,\n        cname: \"TransDecoder\",\n        command:  transdecoder,\n        category: \"post_assembly\",\n        output_dir: transdecoder,\n        inputs: [{ name: \"assembly_fasta\", type: \"contigs\", description: \"Assembly fasta\" }],\n        outputs:  [{ name: \"pep\", type: \"contigs\",  description: \"Pep\"}, { name: \"cds\", type: \"contigs\",  description: \"Cds\"}, { name: \"gff3\", type: \"gff3\", description: \"Gff3\"}, { name: \"bed\", type: \"bed\", description: \"Bed\"}],\n        options:\n          [\n            {\n              name: transdecoder_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      },\n    ],\n  install: {\n    # HMMER: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget http:\/\/eddylab.org\/software\/hmmer\/hmmer-3.2.1.tar.gz\",\n    #   \"tar -xvzf hmmer-3.2.1.tar.gz\",\n    #   \"cd hmmer-3.2.1\",\n    #   \".\/configure --prefix \/opt\/biotools\/\",\n    #   \"make -j 10\",\n    #   \"make install\",\n    #   \"cd easel; make install\",\n    #   \"rm -r ..\/hmmer-3.2.1.tar.gz ..\/hmmer-3.2.1\"\n\n    # ],\n    # transdecoder: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/TransDecoder\/TransDecoder\/archive\/TransDecoder-v5.5.0.tar.gz\",\n    #   \"tar -xvzf TransDecoder-v5.5.0.tar.gz\",\n    #   \"cd bin\",\n    #   \"ln -s \/opt\/biotools\/TransDecoder-v5.5.0\/TransDecoder.LongOrfs TransDecoder.LongOrfs\",\n    #   \"ln -s \/opt\/biotools\/TransDecoder-v5.5.0\/TransDecoder.Predict TransDecoder.Predict\",\n    #   \"rm ..\/TransDecoder-v5.5.0.tar.gz\"\n    # ]\n  },\n  citations:\n    {\n      transdecoder: [\n        \"Haas, BJ. https:\/\/github.com\/TransDecoder\/TransDecoder\",\n      ],\n    },\n}\n"
    }
]