{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_reldist",
  "description": "Calculate the relative distance distribution between two feature files.\n\nbedtools reldist computes the distribution of relative distances between features \nin two genomic datasets. This tool is useful for understanding spatial relationships \nand clustering patterns between different types of genomic features.\n\nThe tool calculates relative distances by measuring how close features in dataset A \nare to the nearest features in dataset B, normalized by the distance between adjacent \nfeatures in dataset B. This provides insights into whether features cluster together \nmore than expected by chance.\n\nThis tool is commonly used for:\n- Analyzing spatial clustering of genomic features\n- Comparing distributions of regulatory elements\n- Quality control of feature calling algorithms\n- Statistical analysis of genomic co-localization\n- Studying relationships between different genomic annotations\n- Identifying non-random spatial patterns in genomic data\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "bed_a": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "First input BED/GFF/VCF file with genomic features.\n\n**Format:** BED, GFF, or VCF file with genomic coordinates\n**Content:** Primary feature set for distance calculation\n**Usage:** Distances will be calculated FROM these features TO features in dataset B\n**Requirements:** Standard genomic coordinate format\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"peaks.bed\"`. "
        },
        "bed_b": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Second input BED/GFF/VCF file with genomic features.\n\n**Format:** BED, GFF, or VCF file with genomic coordinates\n**Content:** Reference feature set for distance calculation\n**Usage:** Distances will be calculated TO these features FROM features in dataset A\n**Requirements:** Standard genomic coordinate format\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"genes.bed\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file with relative distance analysis results.\n\n**Format:** Tab-delimited text file\n**Content:** Either summary statistics or detailed per-interval distances\n**Summary mode:** Distribution bins and frequencies\n**Detail mode:** Individual relative distances for each interval in dataset A\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"relative_distances.txt\"`. ",
          "default": "$id.$key.output.txt"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "detail": {
          "type": "boolean",
          "description": "Report the relative distance for each interval in dataset A.\n\n**Default:** Summary mode (distribution statistics)\n**Detail mode:** Individual relative distance for each feature in A\n**Usage:** Provides granular distance information for downstream analysis\n**Output:** One line per feature in dataset A with its relative distance\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"
    }
  ]
}
