{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "spatial_neighborhood_graph",
  "description": "Calculates a spatial neighborhood graph based on the spatial coordinates.",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input H5MU file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "modality": {
          "type": "string",
          "description": "Which modality from the input MuData file to process.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "input_obsm_spatial_coords": {
          "type": "string",
          "description": "Key in adata.obsm where spatial coordinates are stored",
          "help_text": "Type: `string`, multiple: `False`, default: `\"spatial\"`. ",
          "default": "spatial"
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output H5MU file path.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
          "enum": [
            "gzip",
            "lzf"
          ]
        }
      }
    },
    "spatial neighbors calculation": {
      "title": "Spatial Neighbors Calculation",
      "type": "object",
      "description": "No description",
      "properties": {
        "coord_type": {
          "type": "string",
          "description": "Type of coordinate system",
          "help_text": "Type: `string`, multiple: `False`, default: `\"generic\"`, choices: ``generic`, `grid``. ",
          "enum": [
            "generic",
            "grid"
          ],
          "default": "generic"
        },
        "n_spatial_neighbors": {
          "type": "integer",
          "description": "Depending on `--coord_type`:\n`grid` - number of neighboring tiles.\n`generic` - number of neighborhoods for non-grid data",
          "help_text": "Type: `integer`, multiple: `False`, default: `6`. ",
          "default": 6
        },
        "delaunay": {
          "type": "boolean",
          "description": "Whether to use Delaunay triangulation to determine spatial neighborhood graph.\nOnly used when `--coord_type generic`.\n",
          "help_text": "Type: `boolean`, 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/spatial neighbors calculation"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
