{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "velocyto_to_h5mu",
  "description": "Convert a velocyto loom file to a h5mu file.\n\nIf an input h5mu file is also provided, the velocity\nh5ad object will get added to that h5mu instead.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input_loom": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to the input loom file.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.loom\"`. "
        },
        "input_h5mu": {
          "type": "string",
          "format": "path",
          "description": "If a MuData file is provided, the velocity h5ad object will be added to this file.",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"input.h5mu\"`. "
        },
        "modality": {
          "type": "string",
          "description": "The name of the modality to operate on.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rna_velocity\"`. ",
          "default": "rna_velocity"
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Path to the output MuData file.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "layer_spliced": {
          "type": "string",
          "description": "Output layer for the spliced reads.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"velo_spliced\"`. ",
          "default": "velo_spliced"
        },
        "layer_unspliced": {
          "type": "string",
          "description": "Output layer for the unspliced reads.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"velo_unspliced\"`. ",
          "default": "velo_unspliced"
        },
        "layer_ambiguous": {
          "type": "string",
          "description": "Output layer for the ambiguous reads.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"velo_ambiguous\"`. ",
          "default": "velo_ambiguous"
        },
        "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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
