{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "from_tiledb_to_h5mu",
  "description": "No description",
  "type": "object",
  "$defs": {
    "input database": {
      "title": "Input database",
      "type": "object",
      "description": "Open a tileDB-SOMA database by URI.",
      "properties": {
        "input_uri": {
          "type": "string",
          "description": "A URI pointing to a TileDB-SOMA database.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"s3://bucket/path\"`. "
        },
        "s3_region": {
          "type": "string",
          "description": "Region where the TileDB-SOMA database is hosted.\n",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "endpoint": {
          "type": "string",
          "description": "Custom endpoint to use to connect to S3\n",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "s3_no_sign_request": {
          "type": "boolean",
          "description": "Do not sign S3 requests",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "input_modality": {
          "type": "string",
          "description": "TileDB-SOMA measurement to take the input from.\n",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "input_layers": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Layers to import from TileDB-SOMA database.\n",
          "help_text": "Type: `string`, multiple: `True`, required. "
        }
      }
    },
    "mudata output": {
      "title": "MuData output",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "The output MuData file.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "output_modality": {
          "type": "string",
          "description": "Name of the modality to write the results to.\n",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "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/input database"
    },
    {
      "$ref": "#/$defs/mudata output"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
