{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_complement",
  "description": "Find genomic intervals that are NOT covered by input intervals.\n\nThis tool returns the complement of genomic intervals - the regions\nof the genome that are NOT covered by the input features. Useful for\nfinding gaps, uncovered regions, or background intervals.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input file in BED, GFF, or VCF format.\n\n**BED format:** Standard genomic interval format\n**GFF format:** Gene feature format with annotations\n**VCF format:** Variant call format\n**Requirements:** Should be sorted by chromosome and position for optimal performance\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"covered_regions.bed\"`. "
        },
        "genome": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Genome file defining chromosome names and sizes.\n\n**Format:** Tab-delimited file with chromosome name and size\n**Example line:** chr1  249250621\n**Sources:** Can be created with samtools faidx or UCSC Table Browser\n**Purpose:** Defines the complete genomic space for complement calculation\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"genome.txt\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file with complement intervals.\n\nContains genomic intervals representing the regions NOT covered\nby the input intervals",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"uncovered_regions.bed\"`. ",
          "default": "$id.$key.output.bed"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "limit_chromosomes": {
          "type": "boolean",
          "description": "Limit output to chromosomes present in input file.\n\n**Default:** Output includes all chromosomes from genome file\n**When enabled:** Only output complement for chromosomes that have\nrecords in the input file\n**Use case:** Focus analysis on chromosomes of interest\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"
    }
  ]
}
