{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "neighbors_leiden_umap",
  "description": "Performs neighborhood search, leiden clustering and run umap on an integrated embedding.",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to the sample.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"dataset.h5mu\"`. "
        },
        "obsm_input": {
          "type": "string",
          "description": "The key of the embedding to use as input.",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "modality": {
          "type": "string",
          "description": "Which modality to process.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Destination path to the output.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        }
      }
    },
    "neighbour calculation": {
      "title": "Neighbour calculation",
      "type": "object",
      "description": "No description",
      "properties": {
        "uns_neighbors": {
          "type": "string",
          "description": "In which .uns slot to store various neighbor output objects.",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "obsp_neighbor_distances": {
          "type": "string",
          "description": "In which .obsp slot to store the distance matrix between the resulting neighbors.",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "obsp_neighbor_connectivities": {
          "type": "string",
          "description": "In which .obsp slot to store the connectivities matrix between the resulting neighbors.",
          "help_text": "Type: `string`, multiple: `False`, required. "
        }
      }
    },
    "clustering options": {
      "title": "Clustering options",
      "type": "object",
      "description": "No description",
      "properties": {
        "obs_cluster": {
          "type": "string",
          "description": "Prefix for the .obs keys under which to add the cluster labels",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "leiden_resolution": {
          "type": "array",
          "items": {
            "type": "number"
          },
          "description": "Control the coarseness of the clustering",
          "help_text": "Type: `double`, multiple: `True`, default: `[1.0]`. ",
          "default": [
            1.0
          ]
        }
      }
    },
    "umap options": {
      "title": "Umap options",
      "type": "object",
      "description": "No description",
      "properties": {
        "obsm_umap": {
          "type": "string",
          "description": "In which .obsm slot to store the resulting UMAP embedding.\nWhen not specified, UMAP will not be executed.\n",
          "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/neighbour calculation"
    },
    {
      "$ref": "#/$defs/clustering options"
    },
    {
      "$ref": "#/$defs/umap options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
