{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/amrfinderplus/params.json",
    "title": "AMRFinder+ Module",
    "description": "A module to identify antimicrobial resistance in genes or proteins",
    "type": "object",
    "definitions": {
        "amrfinderplus_parameters": {
            "title": "AMRFinder+ Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "ident_min": {
                    "type": "number",
                    "default": -1,
                    "description": "Minimum proportion of identical amino acids in alignment for hit (0..1)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "coverage_min": {
                    "type": "number",
                    "default": 0.5,
                    "description": "Minimum coverage of the reference protein (0..1)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "organism": {
                    "type": "string",
                    "description": "Taxonomy group to run additional screens against",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "translation_table": {
                    "type": "integer",
                    "default": 11,
                    "description": "NCBI genetic code for translated BLAST",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "amrfinder_noplus": {
                    "type": "boolean",
                    "default": false,
                    "description": "Disable running AMRFinder+ with the --plus option",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "report_common": {
                    "type": "boolean",
                    "default": false,
                    "description": "Report proteins common to a taxonomy group",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "report_all_equal": {
                    "type": "boolean",
                    "default": false,
                    "description": "Report all equally-scoring BLAST and HMM matches",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "amrfinder_opts": {
                    "type": "string",
                    "description": "Extra AMRFinder+ options in quotes.",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/amrfinderplus_parameters"
        }
    ]
}
