{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "agat_sp_statistics",
  "description": "The script provides exhaustive statistics of a gft/gff file. \n\nIf you have isoforms in your file, even if correct, some values calculated\nmight sounds incoherent: e.g. total length mRNA can be superior than the\ngenome size. Because all isoforms length is added... It is why by\ndefault we always compute the statistics twice when there are isoforms,\nonce with the isoforms, once without (In that case we keep the longest\nisoform per locus).\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "gff": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input GTF/GFF file.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.gff\"`. "
        },
        "gs_fasta": {
          "type": "string",
          "format": "path",
          "description": "Genome size directly from a fasta file to compute more statistics.\n",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.fasta\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "The file where the results will be written.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ",
          "default": "$id.$key.output.txt"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "plot": {
          "type": "boolean",
          "description": "When this option is used, an histogram of distribution of the features will be printed in pdf files.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "gs_size": {
          "type": "integer",
          "description": "Genome size in nucleotides to compute more statistics.\n",
          "help_text": "Type: `integer`, multiple: `False`, example: `1000000`. "
        },
        "verbose": {
          "type": "integer",
          "description": "Verbose option",
          "help_text": "Type: `integer`, multiple: `False`, example: `1`. "
        },
        "config": {
          "type": "string",
          "format": "path",
          "description": "AGAT config file",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. "
        }
      }
    },
    "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/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
