{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "popv",
  "description": "Performs popular major vote cell typing on single cell sequence data using multiple algorithms. Note that this is a one-shot version of PopV.",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "Arguments related to the input (aka query) dataset.",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
        },
        "modality": {
          "type": "string",
          "description": "Which modality to process.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "input_layer": {
          "type": "string",
          "description": "Which layer to use",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "input_obs_batch": {
          "type": "string",
          "description": "Key in obs field of input adata for batch information",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "input_var_subset": {
          "type": "string",
          "description": "Subset the input object with this column.",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "input_obs_label": {
          "type": "string",
          "description": "Key in obs field of input adata for label information",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "unknown_celltype_label": {
          "type": "string",
          "description": "If `input_obs_label` is specified, cells with this value will be treated as unknown and will be predicted by the model.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"unknown\"`. ",
          "default": "unknown"
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "Output arguments.",
      "properties": {
        "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"
          ]
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "Other arguments.",
      "properties": {
        "methods": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Methods to call cell types",
          "help_text": "Type: `string`, multiple: `True`, required, example: `[\"knn_on_scvi\";\"scanvi\"]`, choices: ``celltypist`, `knn_on_bbknn`, `knn_on_scanorama`, `knn_on_scvi`, `onclass`, `rf`, `scanvi`, `svm``. "
        }
      }
    },
    "reference": {
      "title": "Reference",
      "type": "object",
      "description": "Arguments related to the reference dataset.",
      "properties": {
        "reference": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "User-provided reference tissue",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"TS_Bladder_filtered.h5ad\"`. "
        },
        "reference_layer": {
          "type": "string",
          "description": "Which layer to use",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "reference_obs_label": {
          "type": "string",
          "description": "Key in obs field of reference AnnData with cell-type information.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"cell_ontology_class\"`. ",
          "default": "cell_ontology_class"
        },
        "reference_obs_batch": {
          "type": "string",
          "description": "Key in obs field of input adata for batch information.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"donor_assay\"`. ",
          "default": "donor_assay"
        }
      }
    },
    "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/arguments"
    },
    {
      "$ref": "#/$defs/reference"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
