{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "from_xenium_to_h5mu",
  "description": "Converts the output from Xenium to a single .h5mu file, where the count matrix is written to the `rna` modality.\nThe following files are expected to be present in the Xenium output bundle:\n├── cell_feature_matrix.h5\n├── cells.parquet\n├── experiment.xenium\n└── metrics_summary.csv\n",
  "type": "object",
  "$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_output_bundle\"`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output .h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"xenium.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "obsm_coordinates": {
          "type": "string",
          "description": "Name of the .obsm slot under which to store the cell centroid coordinates.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"spatial\"`. ",
          "default": "spatial"
        },
        "uns_experiment": {
          "type": "string",
          "description": "Name of the .uns slot under which to store the Xenium experiment specifications.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"xenium_experiment\"`. ",
          "default": "xenium_experiment"
        },
        "uns_metrics": {
          "type": "string",
          "description": "Name of the .uns slot under which to store the summary QC metrics.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"xenium_metrics\"`. ",
          "default": "xenium_metrics"
        },
        "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"
          ]
        }
      }
    },
    "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"
    }
  ]
}
