{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "agat_sq_stat_basic",
  "description": "The script aims to provide basic statistics of a gtf/gff file.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "gff": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Input GTF/GFF file.\n",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input.gff\"]`. "
        },
        "genome_size": {
          "type": "integer",
          "description": "That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type",
          "help_text": "Type: `integer`, multiple: `False`, example: `10000`. "
        },
        "genome_size_fasta": {
          "type": "string",
          "format": "path",
          "description": "That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.fasta\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ",
          "default": "$id.$key.output.txt"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "inflate": {
          "type": "boolean",
          "description": "Inflate the statistics taking into account feature with\nmulti-parents",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "config": {
          "type": "string",
          "format": "path",
          "description": "AGAT config file",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. "
        }
      }
    },
    "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"
    }
  ]
}
