{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "kallisto_quant",
  "description": "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.\n",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "index": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Kallisto genome index.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "output_dir": {
          "type": "string",
          "format": "path",
          "description": "Directory to write output to.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_dir\"`, direction: `output`. ",
          "default": "$id.$key.output_dir"
        },
        "log": {
          "type": "string",
          "format": "path",
          "description": "File containing log information from running kallisto quant",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log\"`, direction: `output`. ",
          "default": "$id.$key.log"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "single": {
          "type": "boolean",
          "description": "Single end mode.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "single_overhang": {
          "type": "boolean",
          "description": "Include reads where unobserved rest of fragment is predicted to lie outside a transcript.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "fr_stranded": {
          "type": "boolean",
          "description": "Strand specific reads, first read forward.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "rf_stranded": {
          "type": "boolean",
          "description": "Strand specific reads, first read reverse.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "fragment_length": {
          "type": "number",
          "description": "The estimated average fragment length.",
          "help_text": "Type: `double`, multiple: `False`. "
        },
        "sd": {
          "type": "number",
          "description": "The estimated standard deviation of the fragment length (default: -l, -s values are estimated \nfrom paired end data, but are required when using --single).\n",
          "help_text": "Type: `double`, multiple: `False`. "
        },
        "plaintext": {
          "type": "boolean",
          "description": "Output plaintext instead of HDF5.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "bootstrap_samples": {
          "type": "integer",
          "description": "Number of bootstrap samples to draw",
          "help_text": "Type: `integer`, multiple: `False`, example: `0`. "
        },
        "seed": {
          "type": "integer",
          "description": "Random seed for bootstrap",
          "help_text": "Type: `integer`, multiple: `False`, example: `42`. "
        }
      }
    },
    "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/input"
    },
    {
      "$ref": "#/$defs/output"
    },
    {
      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
