{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_getfasta",
  "description": "Extract DNA sequences from a FASTA file based on feature coordinates.\n\nGiven intervals specified in BED/GFF/VCF format and a FASTA file, this tool\nextracts the corresponding sequences from the FASTA file. Various output formats\nare supported including FASTA (default), tab-delimited, and BED format with sequences.\n",
  "type": "object",
  "$defs": {
    "input arguments": {
      "title": "Input arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input_fasta": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input FASTA file containing sequences for extraction.\nThe headers in the input FASTA file must exactly match the chromosome\ncolumn in the BED file.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "input_bed": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "BED/GFF/VCF file containing intervals to extract from the FASTA file.\nBED files containing a single region require a newline character\nat the end of the line, otherwise a blank output file is produced.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "rna": {
          "type": "boolean",
          "description": "The FASTA is RNA not DNA",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "processing options": {
      "title": "Processing options",
      "type": "object",
      "description": "No description",
      "properties": {
        "strandedness": {
          "type": "boolean",
          "description": "Force strandedness",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "split": {
          "type": "boolean",
          "description": "When input is in BED12 format, create a separate FASTA entry for each block in a BED12 record.\nBlocks are described in the 11th and 12th columns of the BED format.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "full_header": {
          "type": "boolean",
          "description": "Use full FASTA header",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "output arguments": {
      "title": "Output arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file where the extracted sequences will be written.\nBy default, output is in FASTA format unless --tab or --bed_out is specified.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
        },
        "name": {
          "type": "boolean",
          "description": "Set the FASTA header for each extracted sequence to be the \"name\" and coordinate \ncolumns from the BED feature (format: name::chr:start-end).\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "name_only": {
          "type": "boolean",
          "description": "Set the FASTA header for each extracted sequence to be only the \"name\" \ncolumn from the BED feature.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "tab": {
          "type": "boolean",
          "description": "Report extracted sequences in a tab-delimited format instead of FASTA format.\nOutput format: name<tab>sequence.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "bed_out": {
          "type": "boolean",
          "description": "Report extracted sequences in a tab-delimited BED format instead of FASTA format.\nOutput format: chr<tab>start<tab>end<tab>name<tab>sequence",
          "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/input arguments"
    },
    {
      "$ref": "#/$defs/processing options"
    },
    {
      "$ref": "#/$defs/output arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
