{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "agat_convert_genscan2gff",
  "description": "The script takes a GENSCAN file as input, and will translate it in gff\nformat. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).\n\n**Known problem** \n\nYou must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA\nsequences and does not crash/warn if an header is submited along the\nsequence. e.g If you have an header \">seq\" s-e-q are seen as the 3 first\nnucleotides of the sequence. Then all prediction location are shifted\naccordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html). \nI don't know if there is the same problem elsewhere.)\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "genscan": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input genscan bed file that will be converted.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output GFF file",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ",
          "default": "$id.$key.output.gff"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "source": {
          "type": "string",
          "description": "The source informs about the tool used to produce the data and is stored in 2nd field of a gff file",
          "help_text": "Type: `string`, multiple: `False`, example: `\"Stringtie\"`. "
        },
        "primary_tag": {
          "type": "string",
          "description": "The primary_tag corresponds to the data type and is stored in 3rd field of a gff file",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gene\"`. "
        },
        "inflate_type": {
          "type": "string",
          "description": "Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"exon\"`. "
        },
        "verbose": {
          "type": "boolean",
          "description": "add verbosity",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "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/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
