{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "agat_sq_stat_basic",
"description": "The script aims to provide basic statistics of a gtf/gff file.\n",
"type": "object",
"definitions": {

    
    
    "inputs" : {
    "title": "Inputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "gff": {
                "type":
                "string",
                "description": "Type: List of `file`, required, example: `input.gff`, multiple_sep: `\";\"`. Input GTF/GFF file",
                "help_text": "Type: List of `file`, required, example: `input.gff`, multiple_sep: `\";\"`. Input GTF/GFF file.\n"
            
            }
    

        ,
                "genome_size": {
                "type":
                "integer",
                "description": "Type: `integer`, example: `10000`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type",
                "help_text": "Type: `integer`, example: `10000`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide an INTEGER. Or you can also pass a fasta file using the argument --genome_size_fasta. If both are provided, only the value of --genome_size will be considered.\n"
            
            }
    

        ,
                "genome_size_fasta": {
                "type":
                "string",
                "description": "Type: `file`, example: `genome.fasta`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type",
                "help_text": "Type: `file`, example: `genome.fasta`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide the genome in fasta format. Or you can also pass the size directly as an integer using the argument --genome_size. If you provide the fasta, the genome size will be calculated on the fly. If both are provided, only the value of --genome_size will be considered.\n"
            
            }
    

}
},
    
    
    "outputs" : {
    "title": "Outputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.output.txt`, example: `output.txt`. Output file",
                "help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `output.txt`. Output file. The result is in tabulate format.\n"
            ,
                "default": "$id.$key.output.txt"
            }
    

}
},
    
    
    "arguments" : {
    "title": "Arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "inflate": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Inflate the statistics taking into account feature with\nmulti-parents",
                "help_text": "Type: `boolean_true`, default: `false`. Inflate the statistics taking into account feature with\nmulti-parents. Indeed to avoid redundant information, some gff\nfactorize identical features. e.g: one exon used in two\ndifferent isoform will be defined only once, and will have\nmultiple parent. By default the script count such feature only\nonce. Using the inflate option allows to count the feature and\nits size as many time there are parents.\n"
            ,
                "default": "False"
            }
    

        ,
                "config": {
                "type":
                "string",
                "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file",
                "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n"
            
            }
    

}
},
    
    
    "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": "Type: `string`, required, example: `output/`. Path to an output directory",
                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
            
            }
    

        ,
                "param_list": {
                "type":
                "string",
                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
                "hidden": true
            
            }
    

}
}
},
"allOf": [

    {
    "$ref": "#/definitions/inputs"
    },

    {
    "$ref": "#/definitions/outputs"
    },

    {
    "$ref": "#/definitions/arguments"
    },

    {
    "$ref": "#/definitions/nextflow input-output arguments"
    }
]
}
