{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_links",
  "description": "This tool generates an HTML page containing links to the UCSC Genome Browser\nfor each feature/interval in the input file. This is particularly useful for\nmanually inspecting large sets of genomic annotations or features through\nthe browser interface.\n\n**Default behavior:** Links point to human genome (hg18) on the main UCSC site\n**Customization:** Supports custom mirror sites and different organisms/builds\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input file in BED, GFF, or VCF format containing genomic intervals.\n\nEach feature/interval will be converted to a clickable link pointing\nto the UCSC Genome Browser",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"intervals.bed\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output HTML file containing clickable browser links.\n\nThe generated HTML page will contain one link per input feature,\nformatted for easy navigation to the UCSC Genome Browser.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.html\"`, direction: `output`, example: `\"browser_links.html\"`. ",
          "default": "$id.$key.output.html"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "base_url": {
          "type": "string",
          "description": "Base URL for the UCSC Genome Browser instance.\n\n**Default:** http://genome.ucsc.edu (official UCSC site)\n**Custom mirrors:** Use your institution's mirror URL\n**Example:** http://mymirror.myuniversity.edu\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"http://genome.ucsc.edu\"`. "
        },
        "organism": {
          "type": "string",
          "description": "Target organism for genome browser links.\n\n**Common values:**\n- human (default)\n- mouse\n- rat\n- fly\n- worm\n\nMust match organism names used by your UCSC browser instance.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"human\"`. "
        },
        "database": {
          "type": "string",
          "description": "Genome assembly/build identifier.\n\n**Human examples:** hg19, hg38, hg18 (default)\n**Mouse examples:** mm9, mm10, mm39\n**Other:** Assembly names as recognized by UCSC browser\n\nMust correspond to available assemblies for the specified organism.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"hg18\"`. "
        }
      }
    },
    "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"
    }
  ]
}
