{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/conf/schema/bactopia-tools.json",
    "title": "Bactopia Tools ",
    "description": "Parameters for workflows associated with Bactopia Tools",
    "type": "object",
    "definitions": {
        "input_parameters": {
            "title": "Required Parameters",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "help_text": "",
            "properties": {
                "bactopia": {
                    "type": "string",
                    "description": "The path to bactopia results to use as inputs",
                    "help": "The required inputs will be automatically selected by the subworkflow.",
                    "fa_icon": "fas fa-bacterium"
                }
            }
        },
        "filter_parameters": {
            "title": "Filtering Parameters",
            "type": "object",
            "description": "Use these parameters to specify which samples to include or exclude.",
            "default": "",
            "fa_icon": "fa-solid fa-filter",
            "properties": {
                "include": {
                    "type": "string",
                    "description": "A text file containing sample names (one per line) to include from the analysis",
                    "help": "The expected format is a single sample per line.",
                    "fa_icon": "far fa-square-plus"
                },
                "exclude": {
                    "type": "string",
                    "description": "A text file containing sample names (one per line) to exclude from the analysis",
                    "help": "The expected format is a single sample per line.",
                    "fa_icon": "far fa-square-minus"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_parameters"
        },
        {
            "$ref": "#/definitions/filter_parameters"
        }
    ]
}
