{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_bedtobam",
  "description": "Converts feature records to BAM format.\n\nConverts genomic intervals from BED, GFF, or VCF formats into BAM format,\ncreating aligned sequence records that can be used with standard BAM tools.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input genomic intervals file in BED, GFF, or VCF format.\n\n**Requirements:**\n- BED files must be at least BED4 format (requires name field)\n- File must contain valid genomic coordinates\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.bed\"`. "
        },
        "genome": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Genome file defining chromosome names and sizes.\n\n**Format:** Two-column tab-delimited file:\n```\nchr1    249250621\nchr2    243199373\n```\n\n**Note:** This is NOT a FASTA file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"hg19.genome\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output BAM file containing converted genomic intervals.\n\n**Format:** Standard BAM format (compressed by default)\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bam\"`, direction: `output`, example: `\"output.bam\"`. ",
          "default": "$id.$key.output.bam"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "map_quality": {
          "type": "integer",
          "description": "Set the mapping quality for the BAM records.\n\n**Range:** 0-255 (higher values indicate better quality)\n\n**Default:** 255 (maximum quality)\n",
          "help_text": "Type: `integer`, multiple: `False`, default: `255`. ",
          "default": 255
        },
        "bed12": {
          "type": "boolean",
          "description": "Process BED file as BED12 format with blocked intervals.\n\n**Features:**\n- BAM CIGAR string reflects BED blocks (exons/introns)\n- Useful for representing spliced alignments\n- Requires BED12 format input\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "uncompress_bam": {
          "type": "boolean",
          "description": "Write uncompressed BAM output.\n\n**Default behavior:** Writes compressed BAM\n**Use case:** When downstream tools require uncompressed format\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"
    }
  ]
}
