{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bedtools_groupby",
  "description": "Summarizes a dataset column based upon common column groupings. \nAkin to the SQL \"group by\" command.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "The input BED file to be used.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input_a.bed\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "The output groupby BED file",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"output.bed\"`. ",
          "default": "$id.$key.output.bed"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "groupby": {
          "type": "string",
          "description": "Specify the columns (1-based) for the grouping.\nThe columns must be comma separated.\n- Default: 1,2,3  \n",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "column": {
          "type": "integer",
          "description": "Specify the column (1-based) that should be summarized.\n",
          "help_text": "Type: `integer`, multiple: `False`, required. "
        },
        "operation": {
          "type": "string",
          "description": "Specify the operation that should be applied to opCol.\nValid operations:\n    sum, count, count_distinct, min, max,\n    mean, median, mode, antimode,\n    stdev, sstdev (sample standard dev.),\n    collapse (i.e., print a comma separated list (duplicates allowed)), \n    distinct (i.e., print a comma separated list (NO duplicates allowed)), \n    distinct_sort_num (as distinct, but sorted numerically, ascending), \n    distinct_sort_num_desc (as distinct, but sorted numerically, descending), \n    concat   (i.e., merge values into a single, non-delimited string), \n    freqdesc (i.e., print desc",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "full": {
          "type": "boolean",
          "description": "Print all columns from input file",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "inheader": {
          "type": "boolean",
          "description": "Input file has a header line - the first line will be ignored.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "outheader": {
          "type": "boolean",
          "description": "Print header line in the output, detailing the column names",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "header": {
          "type": "boolean",
          "description": "same as '-inheader -outheader'.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "ignorecase": {
          "type": "boolean",
          "description": "Group values regardless of upper/lower case.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "precision": {
          "type": "integer",
          "description": "Sets the decimal precision for output",
          "help_text": "Type: `integer`, multiple: `False`, default: `5`. ",
          "default": 5
        },
        "delimiter": {
          "type": "string",
          "description": "Specify a custom delimiter for the collapse operations.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\",\"`, example: `\"|\"`. ",
          "default": ","
        }
      }
    },
    "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"
    }
  ]
}
