{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_bed12tobed6",
  "description": "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features.\nFor example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input BED12 file containing blocked features.\n\n**Requirements:**\n- Must be in BED12 format (12 columns)\n- Should contain blocked features (e.g., genes with exons)\n- Blocks are defined by columns 10-12 (blockCount, blockSizes, blockStarts)\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.bed12\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output BED6 file containing discrete features.\n\n**Output format:**\n- Each block from input BED12 becomes a separate BED6 entry\n- Maintains chromosome, strand, and name information\n- Coordinates are adjusted to represent individual blocks\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.bed6\"`, direction: `output`, example: `\"output.bed6\"`. ",
          "default": "$id.$key.output.bed6"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "n_score": {
          "type": "boolean",
          "description": "Force the score to be the 1-based block number from the BED12.\n\n**Default behavior:** Preserves original score from BED12\n**With --n_score:** Sets score to block number (1, 2, 3, etc.)\n",
          "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/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
