{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_expand",
  "description": "Expand rows by splitting comma-separated values into separate rows.\n\nThis tool replicates lines based on columns containing comma-separated values,\ncreating one row for each value. Useful for expanding collapsed data formats\nlike BED12 blocks or multi-value annotations into individual entries.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input file with comma-separated values to expand.\n\n**Format:** Tab-delimited file with one or more columns containing\ncomma-separated values\n**Example:** BED file with comma-separated scores or annotations\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"collapsed_data.bed\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file with expanded rows.\n\nContains one row for each comma-separated value, with other\ncolumns replicated across all expanded rows.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"expanded_data.bed\"`. ",
          "default": "$id.$key.output.bed"
        }
      }
    },
    "expansion options": {
      "title": "Expansion Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "columns": {
          "type": "string",
          "description": "Column(s) to expand (1-based indexing).\n\n**Single column:** Specify one column number (e.g., \"4\")\n**Multiple columns:** Comma-separated list (e.g., \"4,5\")\n**Behavior:** Values in specified columns are split and expanded\n**Requirement:** All specified columns must have same number of values\n",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"4,5\"`. "
        }
      }
    },
    "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/expansion options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
