{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "velocyto",
  "description": "Runs the velocity analysis on a BAM file, outputting a loom file.",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to BAM file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "transcriptome": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to GTF file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "barcode": {
          "type": "string",
          "format": "path",
          "description": "Valid barcodes file, to filter the bam",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "without_umi": {
          "type": "boolean",
          "description": "foo",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Velocyto loom file",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
        },
        "logic": {
          "type": "string",
          "description": "The logic to use for the filtering.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"Default\"`, choices: ``Default`, `Permissive10X`, `Intermediate10X`, `ValidatedIntrons10X`, `Stricter10X`, `ObservedSpanning10X`, `Discordant10X`, `SmartSeq2``. ",
          "enum": [
            "Default",
            "Permissive10X",
            "Intermediate10X",
            "ValidatedIntrons10X",
            "Stricter10X",
            "ObservedSpanning10X",
            "Discordant10X",
            "SmartSeq2"
          ],
          "default": "Default"
        }
      }
    },
    "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"
    }
  ]
}
