[
    {
        "id": "transrate",
        "name": "Transrate",
        "article": "10.1101\/gr.196469.115",
        "website": "http:\/\/hibberdlab.com\/transrate",
        "git": "https:\/\/github.com\/Blahah\/transrate",
        "description": "Transrate is software for de-novo transcriptome assembly quality analysis.",
        "version": "1.0.3",
        "documentation": "http:\/\/hibberdlab.com\/transrate\/getting_started.html",
        "commands": [
            {
                "name": "transrate",
                "cname": "Transrate",
                "command": "transrate",
                "category": "quality",
                "output_dir": "transrate",
                "inputs": [
                    {
                        "name": "assembly_fasta",
                        "type": "contigs",
                        "description": "Assembly fasta"
                    }
                ],
                "outputs": [
                    {
                        "name": "qualityForward",
                        "type": "transrate_dir",
                        "description": "Quality forward directory"
                    }
                ],
                "options": [
                    {
                        "name": "transrate_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "transrate": [
                "TransRate: reference free quality assessment of de-novo transcriptome assemblies (2016). Richard D Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly. Genome Research. doi: http:\/\/dx.doi.org\/10.1101\/gr.196469.115"
            ]
        },
        "yaml": "{\n  id: transrate,\n  name: Transrate,\n  article: \"10.1101\/gr.196469.115\",\n  website: \"http:\/\/hibberdlab.com\/transrate\",\n  git: \"https:\/\/github.com\/Blahah\/transrate\",\n  description: \"Transrate is software for de-novo transcriptome assembly quality analysis.\",\n  version: \"1.0.3\",\n  documentation: \"http:\/\/hibberdlab.com\/transrate\/getting_started.html\",\n  commands:\n    [\n      {\n        name: transrate,\n        cname: \"Transrate\",\n        command:  transrate,\n        category: \"quality\",\n        output_dir: transrate,\n        inputs: [{ name: \"assembly_fasta\", type: \"contigs\", description: \"Assembly fasta\" }],\n        outputs:  [\n          { name: \"qualityForward\", type: \"transrate_dir\",  description: \"Quality forward directory\"}\n        ],\n        options:\n          [\n            {\n              name: transrate_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    # transrate: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/bintray.com\/artifact\/download\/blahah\/generic\/transrate-1.0.3-linux-x86_64.tar.gz\",\n    #   \"tar -xvzf transrate-1.0.3-linux-x86_64.tar.gz\",\n    #   \"cd bin\",\n    #   \"ln -s \/opt\/biotools\/transrate-1.0.3-linux-x86_64\/transrate transrate\",\n    #   \"rm ..\/transrate-1.0.3-linux-x86_64.tar.gz\"\n    # ]\n  },\n  citations:\n    {\n      transrate: [\n        \"TransRate: reference free quality assessment of de-novo transcriptome assemblies (2016). Richard D Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly. Genome Research. doi: http:\/\/dx.doi.org\/10.1101\/gr.196469.115\",\n      ],\n    },\n}\n"
    }
]