{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "from_seurat_to_h5mu",
  "description": "Converts a Seurat file into an H5MU file.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input Seurat file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.rds\"`. "
        },
        "assay": {
          "type": "string",
          "description": "Name of the assay to be mapped.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"RNA\"`. ",
          "default": "RNA"
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "modality": {
          "type": "string",
          "description": "Name of the modality to be created.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output H5MU file",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "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"
          ]
        }
      }
    },
    "conversion parameters": {
      "title": "Conversion parameters",
      "type": "object",
      "description": "No description",
      "properties": {
        "layers_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's Layers to AnnData layers",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"layer\": \"seurat_layer\"}\"`. ",
          "default": "True"
        },
        "obs_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's observation columns to AnnData obs columns",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"obs_field\": \"seurat_observation\"}\"`. ",
          "default": "True"
        },
        "var_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's feature rows to AnnData var columns.\nIf True, all features will be mapped by name",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"var_field\": \"seurat_feature\"}\"`. ",
          "default": "True"
        },
        "uns_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's Misc to AnnData uns",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"uns_field\": \"seurat_Misc\"}\"`. ",
          "default": "True"
        },
        "obsm_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's Embeddings to AnnData obsm fields",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"obsm_field\": \"seurat_Embedding\"}\"`. ",
          "default": "True"
        },
        "varm_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's Loadings to AnnData varm fields",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"varm_field\": \"seurat_Loadings\"}\"`. ",
          "default": "True"
        },
        "obsp_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's Graphs to AnnData obsp fields.\nIf True, all fields will be mapped by name",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"obsp_field\": \"seurat_Graph\"}\"`. ",
          "default": "True"
        },
        "varp_mapping": {
          "type": "string",
          "description": "Mapping of Seurat's Misc to AnnData varp fields",
          "help_text": "Type: `string`, multiple: `False`, default: `\"True\"`, example: `\"{\"varp_field\": \"seurat_Misc\"}\"`. ",
          "default": "True"
        },
        "x_mapping": {
          "type": "string",
          "description": "A string specifying Seurat's Layer to mapped to the .X slot, If not provided, no data will be copied to the .X slot.",
          "help_text": "Type: `string`, multiple: `False`. "
        }
      }
    },
    "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/conversion parameters"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
