{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/iqtree/params.json",
    "title": "IQ-TREE Module",
    "description": "Phylogeny from a multiple sequence alignment using the maxium likelihood algorithm.",
    "type": "object",
    "definitions": {
        "iqtree_parameters": {
            "title": "IQ-TREE Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "iqtree_model": {
                    "type": "string",
                    "description": "Substitution model name",
                    "default": "HKY",
                    "fa_icon": "fas fa-italic"
                },
                "bb": {
                    "type": "integer",
                    "description": "Ultrafast bootstrap replicates",
                    "default": 1000,
                    "fa_icon": "fas fa-hashtag"
                },
                "alrt": {
                    "type": "integer",
                    "description": "SH-like approximate likelihood ratio test replicates",
                    "default": 1000,
                    "fa_icon": "fas fa-hashtag"
                },
                "asr": {
                    "type": "boolean",
                    "default": false,
                    "description": "Ancestral state reconstruction by empirical Bayes",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "iqtree_opts": {
                    "type": "string",
                    "description": "Extra IQ-TREE options in quotes.",
                    "help": "Useful if you would like to fine tune your IQ-TREE analysis.",
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_phylogeny": {
                    "type": "boolean",
                    "default": false,
                    "description": "Skip IQ-TREE execution in subworkflows",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/iqtree_parameters"
        }
    ]
}
