{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/phispy/params.json",
    "title": "PhiSpy Module",
    "description": "A module to predict prophages in bacterial genomes",
    "type": "object",
    "definitions": {
        "phispy_parameters": {
            "title": "PhiSpy Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "phispy_number": {
                    "type": "integer",
                    "default": 5,
                    "description": "Number of consecutive genes in a region of window size that must be prophage genes to be called",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "phispy_mincontigsize": {
                    "type": "integer",
                    "default": 5000,
                    "description": "Minimum contig size (in bp) to be included in the analysis. Smaller contigs will be dropped.",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "phispy_windowsize": {
                    "type": "integer",
                    "default": 30,
                    "description": "Window size of consecutive genes to look through to find phages",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "phispy_nonprophage_genegaps": {
                    "type": "integer",
                    "default": 10,
                    "description": "The number of non phage genes between prophages",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "phispy_phage_genes": {
                    "type": "integer",
                    "default": 1,
                    "description": "The minimum number of genes that must be identified as belonging to a phage for the region to be included",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "phispy_randomforest_trees": {
                    "type": "integer",
                    "default": 500,
                    "description": "Number of trees generated by Random Forest classifier",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "phispy_opts": {
                    "type": "string",
                    "description": "Extra options in quotes for Snippy",
                    "fa_icon": "fas fa-italic"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/phispy_parameters"
        }
    ]
}
