[
    {
        "id": "nanoplot_fastq",
        "name": "nanoplot_fastq",
        "description": "nanoplot is a plotting tool for long read sequencing data and alignments",
        "version": "1.41.6",
        "website": "https:\/\/gigabaseorgigabyte.wordpress.com\/2017\/06\/01\/example-gallery-of-nanoplot\/",
        "git": "https:\/\/github.com\/wdecoster\/NanoPlot",
        "documentation": "https:\/\/gigabaseorgigabyte.wordpress.com\/2017\/06\/01\/example-gallery-of-nanoplot\/",
        "article": "10.1093\/bioinformatics\/bty149",
        "multiqc": "custom",
        "commands": [
            {
                "name": "nanoplot_fastq",
                "cname": "nanoplot on fastq",
                "category": "quality",
                "command": "NanoPlot ",
                "output_dir": "nanoplot",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "stats",
                        "file": "NanoStats.txt",
                        "type": "tsv",
                        "description": "Nanoplot stats"
                    }
                ],
                "options": [
                    {
                        "name": "nanoplot_fastq_threads",
                        "prefix": "-t ",
                        "value": 2,
                        "min": 1,
                        "max": 60,
                        "step": 1,
                        "label": "Specify the number (N=integer) of threads\/cores ",
                        "type": "numeric"
                    },
                    {
                        "name": "nanoplot_fastq_maxlength",
                        "prefix": "--maxlength",
                        "value": 40000,
                        "min": 100,
                        "max": 100000,
                        "step": 10,
                        "label": "Hide reads longer than length specified",
                        "type": "numeric"
                    },
                    {
                        "name": "nanoplot_fastq_minlength",
                        "prefix": "--minlength",
                        "value": 150,
                        "min": 1,
                        "max": 1000,
                        "step": 10,
                        "label": "Hide reads shorter than length specified",
                        "type": "numeric"
                    },
                    {
                        "name": "nanoplot_fastq_minqual",
                        "prefix": "--minqual",
                        "value": 7,
                        "min": 0,
                        "max": 60,
                        "step": 1,
                        "label": "Drop reads with an average quality lower than specified",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "nanoplot": [
                "Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. NanoPack: visualizing and processing long-read sequencing data.Bioinformatics, Volume 34, Issue 15, 01 August 2018, Pages 2666-2669"
            ]
        },
        "yaml": "{\n  id: \"nanoplot_fastq\",\n  name: \"nanoplot_fastq\",\n  description: \"nanoplot is a plotting tool for long read sequencing data and alignments\",\n  version: \"1.41.6\",\n  website: \"https:\/\/gigabaseorgigabyte.wordpress.com\/2017\/06\/01\/example-gallery-of-nanoplot\/\",\n  git: \"https:\/\/github.com\/wdecoster\/NanoPlot\",\n  documentation: \"https:\/\/gigabaseorgigabyte.wordpress.com\/2017\/06\/01\/example-gallery-of-nanoplot\/\",\n  article: \"10.1093\/bioinformatics\/bty149\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: \"nanoplot_fastq\",\n        cname: \"nanoplot on fastq\",\n        category: \"quality\",\n        command: \"NanoPlot \",\n        output_dir: \"nanoplot\",\n        inputs:\n          [\n            { name: \"read\", type: \"reads\" },\n          ],\n        outputs: [\n          {\n            name: \"stats\",\n            file: \"NanoStats.txt\",\n            type: \"tsv\",\n            description: \"Nanoplot stats\",\n          },\n        ],\n        options:\n          [\n            {\n              name: \"nanoplot_fastq_threads\",\n              prefix: \"-t \",\n              value: 2,\n              min: 1,\n              max: 60,\n              step: 1,\n              label: \"Specify the number (N=integer) of threads\/cores \",\n              type: \"numeric\",\n            },\n            {\n              name: \"nanoplot_fastq_maxlength\",\n              prefix: \"--maxlength\",\n              value: 40000,\n              min: 100,\n              max: 100000,\n              step: 10,\n              label: \"Hide reads longer than length specified\",\n              type: \"numeric\",\n            },\n            {\n              name: \"nanoplot_fastq_minlength\",\n              prefix: \"--minlength\",\n              value: 150,\n              min: 1,\n              max: 1000,\n              step: 10,\n              label: \"Hide reads shorter than length specified\",\n              type: \"numeric\",\n            },\n            {\n              name: \"nanoplot_fastq_minqual\",\n              prefix: \"--minqual\",\n              value: 7,\n              min: 0,\n              max: 60,\n              step: 1,\n              label: \"Drop reads with an average quality lower than specified\",\n              type: \"numeric\",\n            },\n          ],\n      },\n    ],\n  install:\n    {\n      # nanoplot: [\n      #   \"pip install seaborn==0.10.1\",\n      #   \"pip install nanoplot \"\n      # ],\n    },\n  citations:\n    {\n      nanoplot: [\n        \"Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. NanoPack: visualizing and processing long-read sequencing data.Bioinformatics, Volume 34, Issue 15, 01 August 2018, Pages 2666-2669\"\n        ],\n    },\n}\n"
    }
]