{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/btyper3/params.json",
    "title": "BTyper3 Module",
    "description": "A module for taxonomic classification of Bacillus cereus group isolates.",
    "type": "object",
    "definitions": {
        "btyper3_parameters": {
            "title": "BTyper3 Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "bt_virulence_identity": {
                    "type": "integer",
                    "default": 70,
                    "description": "Minimum percent amino acid/nucleotide identity threshold for a virulence gene to be considered present",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "bt_virulence_coverage": {
                    "type": "integer",
                    "default": 80,
                    "description": "Minimum percent coverage threshold for a virulence gene to be considered present",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "bt_identity": {
                    "type": "integer",
                    "default": 50,
                    "description": "Minimum percent amino acid identity threshold for a Bt toxin gene to be considered present",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "bt_coverage": {
                    "type": "integer",
                    "default": 70,
                    "description": "Minimum percent coverage threshold for a Bt toxin gene to be considered present",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "bt_overlap": {
                    "type": "integer",
                    "default": 70,
                    "description": "Specify maximum proportion of overlap for overlapping Bt toxin genes to be considered separate genes",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "bt_opts": {
                    "type": "string",
                    "default": "",
                    "description": "Additional options to pass to BTyper3",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/btyper3_parameters"
        }
    ]
}
