{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "split_h5mu",
  "description": "Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. \n",
  "type": "object",
  "$defs": {
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output directory containing multiple h5mu files.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"/path/to/output\"`. ",
          "default": "$id.$key.output"
        },
        "output_files": {
          "type": "string",
          "format": "path",
          "description": "A csv containing the base filename and obs feature by which it was split.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_files.csv\"`, direction: `output`, example: `\"sample_files.csv\"`. ",
          "default": "$id.$key.output_files.csv"
        },
        "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"
          ]
        }
      }
    },
    "input & specifications": {
      "title": "Input & specifications",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to a single .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"
        },
        "obs_feature": {
          "type": "string",
          "description": "The .obs column to split the mudata on.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"celltype\"`. "
        },
        "drop_obs_nan": {
          "type": "boolean",
          "description": "Whether to drop all .obs columns that contain only nan values after splitting.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "ensure_unique_filenames": {
          "type": "boolean",
          "description": "Append number suffixes to ensure unique filenames after sanitizing obs feature values.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": 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/outputs"
    },
    {
      "$ref": "#/$defs/input & specifications"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
