{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "from_spaceranger_to_h5mu",
  "description": "Converts the output bundle from spaceranger into an h5mu file.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Convert spatial data resulting from Aviti Teton sequencers that have been processed by the Element Biosciences cells2stats workflow to H5MU format.\n\nThis component processes cells2stats count matrices to create a standardized H5MU file for downstream analysis.\n\nThe component reads:\n- Parquet file containing the count matrix and metadata\n- Panel.json with target and batch information\n\nAnd outputs an H5MU file with:\n- Count data as the main .X matrix\n- Spatial coordinates in obsm\n- Cell Paint intensities in obsm (optional)\n- Nuclear count data as a layer (optional)\n- CellProfiler morphology metrics in obsm (optional)\n- Unassigned targets in obsm (optional)\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"spaceranger_output\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "modality": {
          "type": "string",
          "description": "Name of the modality under which to store the data.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "uns_metrics": {
          "type": "string",
          "description": "Name of the .uns slot under which to QC metrics (if any).",
          "help_text": "Type: `string`, multiple: `False`, default: `\"metrics_spaceranger\"`. ",
          "default": "metrics_spaceranger"
        },
        "uns_probe_set": {
          "type": "string",
          "description": "Name of the .uns slot under which to store probe set information (if any).",
          "help_text": "Type: `string`, multiple: `False`, default: `\"probe_set\"`. ",
          "default": "probe_set"
        },
        "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"
        },
        "output_type": {
          "type": "string",
          "description": "Which Spaceranger output to use for converting to h5mu.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"filtered\"`, choices: ``raw`, `filtered``. ",
          "enum": [
            "raw",
            "filtered"
          ],
          "default": "filtered"
        },
        "output_compression": {
          "type": "string",
          "description": "Compression to use when writing the h5mu file.",
          "help_text": "Type: `string`, multiple: `False`, 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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
