{
"$schema": "http://json-schema.org/draft-07/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 \"\u003eseq\" 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\u0027t know if there is the same problem elsewhere.)\n",
"type": "object",
"definitions": {

    
    
    "inputs" : {
    "title": "Inputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "genscan": {
                "type":
                "string",
                "description": "Type: `file`, required. Input genscan bed file that will be converted",
                "help_text": "Type: `file`, required. Input genscan bed file that will be converted."
            
            }
    

}
},
    
    
    "outputs" : {
    "title": "Outputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file",
                "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file. If no output file is specified, the output will be written to STDOUT."
            ,
                "default": "$id.$key.output.gff"
            }
    

}
},
    
    
    "arguments" : {
    "title": "Arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "source": {
                "type":
                "string",
                "description": "Type: `string`, example: `Stringtie`. 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`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]\n"
            
            }
    

        ,
                "primary_tag": {
                "type":
                "string",
                "description": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file",
                "help_text": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
            
            }
    

        ,
                "inflate_type": {
                "type":
                "string",
                "description": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon]",
                "help_text": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n"
            
            }
    

        ,
                "verbose": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. add verbosity",
                "help_text": "Type: `boolean_true`, default: `false`. add verbosity"
            ,
                "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"
    }
]
}
