{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_bedpetobam",
  "description": "Convert BEDPE (paired-end BED) intervals to BAM format.\n\nThis tool converts genomic paired-end interval data into BAM alignment format,\nwhere each BEDPE record becomes a pair of BAM alignment records representing\nthe paired-end reads.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input file in BEDPE format.\n\n**BEDPE format:** Tab-delimited with 10 columns:\nchrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2\n\n**Requirements:** Represents paired-end genomic intervals\n**Coordinate system:** 0-based coordinates\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"intervals.bedpe\"`. "
        },
        "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**Purpose:** Required for BAM header creation\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 BAM file.\n\nContains converted BEDPE intervals as paired BAM alignment records\nsuitable for visualization and downstream analysis of paired-end data.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bam\"`, direction: `output`, example: `\"intervals.bam\"`. ",
          "default": "$id.$key.output.bam"
        }
      }
    },
    "bam options": {
      "title": "BAM Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "mapq": {
          "type": "integer",
          "description": "Set the mapping quality for BAM records.\n\n**Range:** 0-255 (typical values)\n**Default:** 255 (maximum quality)\n**Purpose:** MAPQ field in BAM format\n",
          "help_text": "Type: `integer`, multiple: `False`, default: `255`, example: `60`. ",
          "default": 255
        },
        "ubam": {
          "type": "boolean",
          "description": "Write uncompressed BAM output.\n\n**Default:** Compressed BAM output\n**Use case:** When compression is not needed or causes issues\n**File size:** Significantly larger output files\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/bam options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
