{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "agat_convert_bed2gff",
  "description": "The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "bed": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input bed file that will be converted.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.bed\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output GFF file",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ",
          "default": "$id.$key.output.gff"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "source": {
          "type": "string",
          "description": "The source informs about the tool used to produce the data and is stored in 2nd field of a gff file",
          "help_text": "Type: `string`, multiple: `False`, example: `\"Stringtie\"`. "
        },
        "primary_tag": {
          "type": "string",
          "description": "The primary_tag corresponds to the data type and is stored in 3rd field of a gff file",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gene\"`. "
        },
        "inflate_off": {
          "type": "boolean",
          "description": "By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag)",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "inflate_type": {
          "type": "string",
          "description": "Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"exon\"`. "
        },
        "verbose": {
          "type": "boolean",
          "description": "add verbosity",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "config": {
          "type": "string",
          "format": "path",
          "description": "Input 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"
    }
  ]
}
