{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "agat_convert_embl2gff",
"description": "The script takes an EMBL file as input, and will translate it in gff format.\n",
"type": "object",
"definitions": {

    
    
    "inputs" : {
    "title": "Inputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "embl": {
                "type":
                "string",
                "description": "Type: `file`, required, example: `input.embl`. Input EMBL file that will be read",
                "help_text": "Type: `file`, required, example: `input.embl`. Input EMBL file that will be read."
            
            }
    

}
},
    
    
    "outputs" : {
    "title": "Outputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file",
                "help_text": "Type: `file`, 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": {
    
        
                "emblmygff3": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Means that the EMBL flat file comes from the EMBLmyGFF3 software",
                "help_text": "Type: `boolean_true`, default: `false`. Means that the EMBL flat file comes from the EMBLmyGFF3 software. This is an EMBL format dedicated for submission and contains particularity to deal with. This parameter is needed to get a proper sequence id in the GFF3 from an embl made with EMBLmyGFF3.\n"
            ,
                "default": "False"
            }
    

        ,
                "primary_tag": {
                "type":
                "string",
                "description": "Type: List of `string`, example: `tag1;tag2`, multiple_sep: `\";\"`. List of \"primary tag\"",
                "help_text": "Type: List of `string`, example: `tag1;tag2`, multiple_sep: `\";\"`. List of \"primary tag\". Useful to discard or keep specific features. Multiple tags must be comma-separated.\n"
            
            }
    

        ,
                "discard": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Means that primary tags provided by the option \"primary_tag\" will be discarded",
                "help_text": "Type: `boolean_true`, default: `false`. Means that primary tags provided by the option \"primary_tag\" will be discarded.\n"
            ,
                "default": "False"
            }
    

        ,
                "keep": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Means that only primary tags provided by the option \"primary_tag\" will be kept",
                "help_text": "Type: `boolean_true`, default: `false`. Means that only primary tags provided by the option \"primary_tag\" will be kept.\n"
            ,
                "default": "False"
            }
    

        ,
                "config": {
                "type":
                "string",
                "description": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file",
                "help_text": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". 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"
    }
]
}
