{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "find_neighbors",
  "description": "Compute a neighborhood graph of observations [McInnes18].\n\nThe neighbor search efficiency of this heavily relies on UMAP [McInnes18], which also provides a method for estimating connectivities of data points - the connectivity of the manifold (method=='umap'). If method=='gauss', connectivities are computed according to [Coifman05], in the adaption of [Haghverdi16].\n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "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 from the input MuData file to process.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna\"`. ",
          "default": "rna"
        },
        "obsm_input": {
          "type": "string",
          "description": "Which .obsm slot to use as a starting PCA embedding.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"X_pca\"`. ",
          "default": "X_pca"
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output h5mu file containing the found neighbors.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "uns_output": {
          "type": "string",
          "description": "Mandatory .uns slot to store various neighbor output objects.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"neighbors\"`. ",
          "default": "neighbors"
        },
        "obsp_distances": {
          "type": "string",
          "description": "In which .obsp slot to store the distance matrix between the resulting neighbors.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"distances\"`. ",
          "default": "distances"
        },
        "obsp_connectivities": {
          "type": "string",
          "description": "In which .obsp slot to store the connectivities matrix between the resulting neighbors.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"connectivities\"`. ",
          "default": "connectivities"
        },
        "metric": {
          "type": "string",
          "description": "The distance metric to be used in the generation of the nearest neighborhood network.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"euclidean\"`, choices: ``cityblock`, `cosine`, `euclidean`, `l1`, `l2`, `manhattan`, `braycurtis`, `canberra`, `chebyshev`, `correlation`, `dice`, `hamming`, `jaccard`, `kulsinski`, `mahalanobis`, `minkowski`, `rogerstanimoto`, `russellrao`, `seuclidean`, `sokalmichener`, `sokalsneath`, `sqeuclidean`, `yule``. ",
          "enum": [
            "cityblock",
            "cosine",
            "euclidean",
            "l1",
            "l2",
            "manhattan",
            "braycurtis",
            "canberra",
            "chebyshev",
            "correlation",
            "dice",
            "hamming",
            "jaccard",
            "kulsinski",
            "mahalanobis",
            "minkowski",
            "rogerstanimoto",
            "russellrao",
            "seuclidean",
            "sokalmichener",
            "sokalsneath",
            "sqeuclidean",
            "yule"
          ],
          "default": "euclidean"
        },
        "num_neighbors": {
          "type": "integer",
          "description": "The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation",
          "help_text": "Type: `integer`, multiple: `False`, default: `15`. ",
          "default": 15
        },
        "seed": {
          "type": "integer",
          "description": "A random seed.",
          "help_text": "Type: `integer`, multiple: `False`, default: `0`. ",
          "default": 0
        },
        "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/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
