{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "from_xenium_to_spatialdata",
  "description": "Converts the output from 10X Genomics Xenium dataset into a SpatialData objcet.\nBy default, the following files will be converted:\n  - `experiment.xenium`: File containing specifications.\n  - `nucleus_boundaries.parquet`: Polygons of nucleus boundaries.\n  - `cell_boundaries.parquet`: Polygons of cell boundaries.\n  - `transcripts.parquet`: File containing transcripts.\n  - `cell_feature_matrix.h5`: File containing cell feature matrix.\n  - `cells.parquet`: File containing cell metadata.\n  - `morphology_mip.ome.tif`: File containing morphology mip.\n  - `morphology_focus.ome.tif`: File containing morphology focus.\n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input folder",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"xenium_data\"`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Zarr directory where the SpatialData object will be stored",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.zarr\"`, direction: `output`, example: `\"xenium_data.zarr\"`. ",
          "default": "$id.$key.output.zarr"
        },
        "cells_boundaries": {
          "type": "boolean",
          "description": "Whether to read cell boundaries (polygons).",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "nucleus_boundaries": {
          "type": "boolean",
          "description": "Whether to read nucleus boundaries (polygons).",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "cells_as_circles": {
          "type": "boolean",
          "description": "Whether to read cells also as circles (the center and the radius of each circle is computed from the corresponding labels cell).",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "cells_labels": {
          "type": "boolean",
          "description": "Whether to read cell labels (raster)",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "transcripts": {
          "type": "boolean",
          "description": "Whether to read transcripts.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "nucleus_labels": {
          "type": "boolean",
          "description": "Whether to read nucleus labels (raster)",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "morphology_mip": {
          "type": "boolean",
          "description": "Whether to read the morphology mip image (available in versions < 2.0.0).",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "morphology_focus": {
          "type": "boolean",
          "description": "Whether to read the morphology focus image.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "aligned_images": {
          "type": "boolean",
          "description": "Whether to also parse, when available, additional H&E or IF aligned images",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "cells_table": {
          "type": "boolean",
          "description": "Whether to read the cell annotations in the AnnData table.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "n_jobs": {
          "type": "integer",
          "description": "",
          "help_text": "Type: `integer`, multiple: `False`, default: `1`. ",
          "default": 1
        }
      }
    },
    "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/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
