{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "tfidf",
  "description": "Perform TF-IDF normalization of the data (typically, ATAC).\n\nTF-IDF stands for \"term frequency - inverse document frequency\". It is a technique from natural language processing analysis.\nIn the context of ATAC data, \"terms\" are the features (genes) and \"documents\" are the observations (cells). \nTF-IDF normalization is applied to single-cell ATAC-seq data to highlight the importance of specific genomic regions (typically peaks)\nacross different cells while down-weighting regions that are commonly accessible across many cells. \n",
  "type": "object",
  "$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: `\"atac\"`. ",
          "default": "atac"
        },
        "input_layer": {
          "type": "string",
          "description": "Input layer to use",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
        },
        "output_layer": {
          "type": "string",
          "description": "Output layer to use.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"tfidf\"`. ",
          "default": "tfidf"
        },
        "scale_factor": {
          "type": "integer",
          "description": "Scale factor to multiply the TF-IDF matrix by.",
          "help_text": "Type: `integer`, multiple: `False`, default: `10000`. ",
          "default": 10000
        },
        "log_idf": {
          "type": "boolean",
          "description": "Whether to log-transform IDF term.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "log_tf": {
          "type": "boolean",
          "description": "Whether to log-transform TF term.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        },
        "log_tfidf": {
          "type": "boolean",
          "description": "Whether to log-transform TF*IDF term (False by default)",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "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"
    }
  ]
}
