{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "rseqc_inferexperiment",
  "description": "Infer strandedness from sequencing reads\n",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "input_file": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "input alignment file in BAM or SAM format",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "refgene": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Reference gene model in bed format",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output file (txt) of strandness report.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"$id.strandedness.txt\"`. ",
          "default": "$id.$key.output.txt"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "sample_size": {
          "type": "integer",
          "description": "Number of reads sampled from SAM/BAM file",
          "help_text": "Type: `integer`, multiple: `False`, example: `200000`. "
        },
        "mapq": {
          "type": "integer",
          "description": "Minimum mapping quality (phred scaled) to determine uniquely mapped reads",
          "help_text": "Type: `integer`, multiple: `False`, example: `30`. "
        }
      }
    },
    "nextflow input-output arguments": {
      "title": "Nextflow input-output arguments",
      "type": "object",
      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
      "properties": {
        "publish_dir": {
          "type": "string",
          "description": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/input"
    },
    {
      "$ref": "#/$defs/output"
    },
    {
      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
