{
    "schema":"https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/draft-1/schemas/tool.json",
    "inputs": {
        "required": [
            "stages"
        ],
        "type": "object",
        "properties": {
            "$mixin": "tmap.json#mixins/global",
            "stages": {
                "minItems": 1,
                "items": {
                    "required": [
                        "stageId",
                        "algos"
                    ],
                    "type": "object",
                    "properties": {
                        "stageId": {
                            "adapter": {
                                "prefix": "stage",
                                "separator": "",
                                "order": 0
                            },
                            "type": "integer"
                        },
                        "stageOption1": {
                            "adapter": {
                                "prefix": "-n",
                                "order": 1
                            },
                            "type": "boolean"
                        },
                        "algos": {
                            "minItems": 1,
                            "items": {
                                "oneOf": [
                                    {
                                        "$ref": "tmap.json#algos/map1"
                                    },
                                    {
                                        "$ref": "tmap.json#algos/map2"
                                    },
                                    {
                                        "$ref": "tmap.json#algos/map3"
                                    },
                                    {
                                        "$ref": "tmap.json#algos/map4"
                                    }
                                ],
                                "type": "object"
                            },
                            "adapter": {
                                "order": 2
                            },
                            "type": "array"
                        }
                    }
                },
                "adapter": {
                    "order": 2
                },
                "type": "array"
            }
        }
    },
    "adapter": {
        "baseCmd": [
            "tmap",
            "mapall"
        ],
        "stdin": { "$job": "#inputs/reads/path" },
        "stdout": "output.sam"
    },
    "outputs": {
        "required": [
            "sam"
        ],
        "type": "object",
        "properties": {
            "sam": {
                "adapter": {
                    "glob": "output.sam"
                },
                "type": "file"
            }
        }
    }
}