{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "from_h5mu_to_spatialdata",
  "description": "Reads in an H5MU file and saves it as a SpatialData Zarr store. The selected\nmodality in the MuData is stored as the main table in the SpatialData object.\nIf a matching existing SpatialData is provided, it will be used to fill the\nremaining SpatialData slots.\n  \n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "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`, example: `\"input.h5mu\"`. "
        },
        "input_spatialdata": {
          "type": "string",
          "format": "path",
          "description": "An optional existing SpatialData Zarr store to fill remaining slots from.",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"existing.zarr\"`. "
        },
        "modality": {
          "type": "string",
          "description": "The modality in the MuData to be used as the main table in the SpatialData object.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "The path to the output SpatialData Zarr store.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.zarr\"`, direction: `output`, example: `\"output.zarr\"`. ",
          "default": "$id.$key.output.zarr"
        }
      }
    },
    "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"
    }
  ]
}
