[
    {
        "id": "mitoz_findmitoscaf",
        "name": "MitoZ find mito scaffold",
        "article": "10.1093\/nar\/gkz173",
        "website": "https:\/\/github.com\/linzhi2013\/MitoZ",
        "git": "https:\/\/github.com\/linzhi2013\/MitoZ",
        "description": "A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes",
        "version": "3.5",
        "documentation": "https:\/\/github.com\/linzhi2013\/MitoZ",
        "multiqc": "custom",
        "commands": [
            {
                "name": "mitoz_findmitoscaf",
                "cname": "Mitoz find mitos scafold",
                "command": "mitoz findmitoscaf ",
                "category": "find_mito_scaffold",
                "output_dir": "mitoz_findmitoscaf",
                "inputs": [
                    {
                        "name": "fasta",
                        "type": "contigs"
                    }
                ],
                "outputs": [
                    {
                        "name": "mitogenome",
                        "type": "contigs",
                        "file": "mitoz_findmitoscaf.mitogenome.fa",
                        "description": "The mitochondrial sequences from each Kmer assembly"
                    },
                    {
                        "name": "readme",
                        "type": "txt",
                        "file": "README.txt",
                        "description": "Readme with all output files explained"
                    }
                ],
                "options": [
                    {
                        "name": "mitoz_findmitoscaf_threads",
                        "prefix": "--thread_number",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "mitoz_findmitoscaf_minabundance",
                        "prefix": "--min_abundance",
                        "type": "numeric",
                        "value": 10,
                        "min": 2,
                        "max": "NA",
                        "step": 1,
                        "label": "the minimum abundance of sequence required"
                    },
                    {
                        "name": "mitoz_findmitoscaf_clade",
                        "type": "radio",
                        "value": "Arthropoda",
                        "choices": [
                            {
                                "Arthropoda": "Arthropoda"
                            },
                            {
                                "Chordata": "Chordata"
                            },
                            {
                                "Echinodermata": "Echinodermata"
                            },
                            {
                                "Annelida-segmented-worms": "Annelida-segmented-worms"
                            },
                            {
                                "Bryozoa": "Bryozoa"
                            },
                            {
                                "Mollusca": "Mollusca"
                            },
                            {
                                "Nematoda": "Nematoda"
                            },
                            {
                                "Nemertea-ribbon-worms": "Nemertea-ribbon-worms"
                            },
                            {
                                "Porifera-sponges": "Porifera-sponges"
                            }
                        ],
                        "label": "Taxa group for MitoZ : "
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "mitoz": [
                "Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, , gkz173, https:\/\/doi.org\/10.1093\/nar\/gkz173"
            ]
        },
        "yaml": "{\n  id: mitoz_findmitoscaf,\n  name: MitoZ find mito scaffold,\n  article: 10.1093\/nar\/gkz173,\n  website: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n  git: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n  description: \"A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes\",\n  version: \"3.5\",\n  documentation: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: mitoz_findmitoscaf,\n        cname: \"Mitoz find mitos scafold\",\n        command: \"mitoz findmitoscaf \",\n        category: \"find_mito_scaffold\",\n        output_dir: mitoz_findmitoscaf,\n        inputs: [{ name: fasta, type: \"contigs\" }],\n        outputs:\n          [\n            { name: mitogenome, type: \"contigs\", file: \"mitoz_findmitoscaf.mitogenome.fa\", description: \"The mitochondrial sequences from each Kmer assembly\" },\n            { name: readme, type: \"txt\", file: \"README.txt\", description: \"Readme with all output files explained\" }\n          ],\n        options:\n          [\n            {\n              name: mitoz_findmitoscaf_threads,\n              prefix: --thread_number,\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              name: mitoz_findmitoscaf_minabundance,\n              prefix: --min_abundance,\n              type: numeric,\n              value: 10,\n              min: 2,\n              max: NA,\n              step: 1,\n              label: \"the minimum abundance of sequence required\",\n            },\n            {\n              name: \"mitoz_findmitoscaf_clade\",\n              type: \"radio\",\n              value: \"Arthropoda\",\n              choices: [\n                Arthropoda: Arthropoda,\n                Chordata: Chordata, \n                Echinodermata: Echinodermata,\n                Annelida-segmented-worms: Annelida-segmented-worms,\n                Bryozoa: Bryozoa,\n                Mollusca: Mollusca,\n                Nematoda: Nematoda,\n                Nemertea-ribbon-worms: Nemertea-ribbon-worms,\n                Porifera-sponges: Porifera-sponges\n              ],\n              label: \"Taxa group for MitoZ : \",\n            },\n          ],\n      },\n    ],\n  install: {\n    # mitoz3.5: [\n    #   \"cd \/opt\/biotools\",\n    #   \"singularity pull MitoZ_v3.5.sif docker:\/\/guanliangmeng\/mitoz:3.5\",\n    # ]\n  },\n  citations:  {\n    mitoz: [\n      \"Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, , gkz173, https:\/\/doi.org\/10.1093\/nar\/gkz173\"\n    ],\n\n  }\n}\n"
    }
]