{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_cluster",
  "description": "Cluster overlapping or nearby genomic intervals.\n\nThis tool groups genomic intervals into clusters based on overlap\nor proximity within a specified distance. Each cluster is assigned\na unique cluster ID, making it useful for analyzing genomic feature\ndistributions and relationships.\n",
  "type": "object",
  "$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:** Must be sorted by chromosome and position\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"intervals.bed\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file with cluster assignments.\n\nContains original intervals with an additional column showing\nthe cluster ID for each interval",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"clustered.bed\"`. ",
          "default": "$id.$key.output.bed"
        }
      }
    },
    "clustering options": {
      "title": "Clustering Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "distance": {
          "type": "integer",
          "description": "Maximum distance between features for clustering.\n\n**Default:** 0 (only overlapping and book-ended features clustered)\n**Positive values:** Cluster features within specified distance\n**Use case:** Group nearby but non-overlapping features\n",
          "help_text": "Type: `integer`, multiple: `False`, default: `0`, example: `1000`. ",
          "default": 0
        },
        "strand": {
          "type": "boolean",
          "description": "Force strandedness in clustering.\n\n**Default:** Clustering ignores strand information\n**When enabled:** Only cluster features on the same strand\n**Use case:** Strand-specific analysis of genomic features\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/clustering options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
