{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_summary",
  "description": "Report summary statistics of genomic intervals in a file.\n\nbedtools summary analyzes genomic intervals and provides comprehensive statistics \nincluding total number of features, total length covered, average feature size, \nand other descriptive metrics. This tool is essential for quality control and \nexploratory data analysis of genomic datasets, helping researchers understand \nthe distribution and characteristics of their interval data.\n\nThis tool is commonly used for:\n- Quality control assessment of genomic interval datasets\n- Exploratory data analysis of ChIP-seq peaks, gene annotations, or variant calls\n- Comparative analysis of interval characteristics between samples\n- Data preprocessing and validation before downstream analysis\n- Generating summary reports for genomic studies\n- Statistical characterization of genomic features\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input file containing genomic intervals for statistical analysis.\n\n**Format:** BED, GFF, VCF, or BAM file with genomic coordinates\n**Content:** Genomic intervals to be analyzed for summary statistics\n**Usage:** Each interval contributes to the overall statistical summary\n**Requirements:** Standard genomic interval format with chromosome, start, end coordinates\n**Analysis:** Statistics computed across all intervals in the file\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"genomic_features.bed\"`. "
        },
        "genome": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Genome file with chromosome names and lengths.\n\n**Format:** Tab-delimited file with chromosome names and sizes\n**Structure:** Each line contains: <chromName><TAB><chromSize>\n**Purpose:** Provides reference genome context for statistical calculations\n**Example lines:** \"chr1\\t249250621\" or \"chr2\\t243199373\"\n**Usage:** Used to calculate genome coverage percentages and context statistics\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 summary statistics of the genomic intervals.\n\n**Format:** Tab-delimited text file with statistical metrics\n**Content:** Comprehensive summary including count, total length, average size, etc.\n**Columns:** Various statistical measures of the interval dataset\n**Usage:** Results suitable for further analysis or reporting\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"interval_summary.txt\"`. ",
          "default": "$id.$key.output.txt"
        }
      }
    },
    "analysis options": {
      "title": "Analysis Options",
      "type": "object",
      "description": "No description",
      "properties": {}
    },
    "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/analysis options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
