{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/rgi/main/params.json",
    "title": "RGI Module",
    "description": "A module for predicxting antibiotic resistance in assemblies",
    "type": "object",
    "definitions": {
        "rgi_parameters": {
            "title": "RGI Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "use_diamond": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use DIAMOND for alignments instead of BLAST",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "include_loose": {
                    "type": "boolean",
                    "default": false,
                    "description": "Include loose hits in addition to strict and perfect hits",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "exclude_nudge": {
                    "type": "boolean",
                    "default": false,
                    "description": "Exclude hits nudged from loose to strict hits",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "rgi_frequency": {
                    "type": "boolean",
                    "default": false,
                    "description": "Represent samples based on resistance profile",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "rgi_category": {
                    "type": "string",
                    "default": "",
                    "description": "Organize resistance genes based on a category",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": [
                        "drug_class",
                        "resistance_mechanism",
                        "gene_family"
                    ],
                    "hidden": true
                },
                "rgi_cluster": {
                    "type": "string",
                    "default": "",
                    "description": "Use SciPy's hiearchical clustering algorithm to cluster rows (AMR genes) or columns (samples)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": [
                        "samples",
                        "genes",
                        "both"
                    ],
                    "hidden": true
                },
                "rgi_display": {
                    "type": "string",
                    "default": "plain",
                    "description": "Specify display options for categories",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": [
                        "plain",
                        "fill",
                        "text"
                    ],
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/rgi_parameters"
        }
    ]
}
