{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "scanorama",
  "description": "Use Scanorama to integrate different experiments.\n",
  "type": "object",
  "$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"
        },
        "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"
        },
        "obs_batch": {
          "type": "string",
          "description": "Column name discriminating between your batches.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"batch\"`. ",
          "default": "batch"
        },
        "obsm_input": {
          "type": "string",
          "description": "Basis obsm slot to run scanorama on.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"X_pca\"`. ",
          "default": "X_pca"
        },
        "obsm_output": {
          "type": "string",
          "description": "The name of the field in adata.obsm where the integrated embeddings will be stored after running this function",
          "help_text": "Type: `string`, multiple: `False`, default: `\"X_scanorama\"`. ",
          "default": "X_scanorama"
        },
        "knn": {
          "type": "integer",
          "description": "Number of nearest neighbors to use for matching.",
          "help_text": "Type: `integer`, multiple: `False`, default: `20`. ",
          "default": 20
        },
        "batch_size": {
          "type": "integer",
          "description": "The batch size used in the alignment vector computation",
          "help_text": "Type: `integer`, multiple: `False`, default: `5000`. ",
          "default": 5000
        },
        "sigma": {
          "type": "number",
          "description": "Correction smoothing parameter on Gaussian kernel.",
          "help_text": "Type: `double`, multiple: `False`, default: `15.0`. ",
          "default": 15.0
        },
        "approx": {
          "type": "boolean",
          "description": "Use approximate nearest neighbors with Python annoy; greatly speeds up matching runtime.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "alpha": {
          "type": "number",
          "description": "Alignment score minimum cutoff",
          "help_text": "Type: `double`, multiple: `False`, default: `0.1`. ",
          "default": 0.1
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata H5 files.\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"
    }
  ]
}
