{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "agat_sp_filter_feature_from_kill_list",
  "description": "Remove features based on a kill list. The default behaviour is to look at the features's ID. \nIf the feature has an ID (case insensitive) listed among the kill list it will be removed.\nRemoving a level1 or level2 feature will automatically remove all linked subfeatures, and \nremoving all children of a feature will automatically remove this feature too.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "gff": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input GFF3 file that will be read.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "kill_list": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Text file containing the kill list",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"kill_list.txt\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Path to the output GFF file that contains filtered features",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "type": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Primary tag option, case insensitive, list",
          "help_text": "Type: `string`, multiple: `True`. "
        },
        "attribute": {
          "type": "string",
          "description": "Attribute tag to specify the attribute to analyse",
          "help_text": "Type: `string`, multiple: `False`, example: `\"ID\"`. "
        },
        "config": {
          "type": "string",
          "format": "path",
          "description": "AGAT config file",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. "
        },
        "verbose": {
          "type": "boolean",
          "description": "Verbose option for debugging purpose.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "nextflow input-output arguments": {
      "title": "Nextflow input-output arguments",
      "type": "object",
      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
      "properties": {
        "publish_dir": {
          "type": "string",
          "description": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
