{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "bedtools_getfasta",
"description": "Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.",
"type": "object",
"definitions": {

    
    
    "input arguments" : {
    "title": "Input arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input_fasta": {
                "type":
                "string",
                "description": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file",
                "help_text": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file.\nThe headers in the input FASTA file must exactly match the chromosome column in the BED file.\n"
            
            }
    

        ,
                "input_bed": {
                "type":
                "string",
                "description": "Type: `file`. BED file containing intervals to extract from the FASTA file",
                "help_text": "Type: `file`. BED file containing intervals to extract from the FASTA file.\nBED files containing a single region require a newline character\nat the end of the line, otherwise a blank output file is produced.\n"
            
            }
    

        ,
                "rna": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA",
                "help_text": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA. Reverse complementation handled accordingly.\n"
            ,
                "default": "False"
            }
    

}
},
    
    
    "run arguments" : {
    "title": "Run arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "strandedness": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Force strandedness",
                "help_text": "Type: `boolean_true`, default: `false`. Force strandedness. If the feature occupies the antisense strand, the output sequence will\nbe reverse complemented. By default strandedness is not taken into account.\n"
            ,
                "default": "False"
            }
    

}
},
    
    
    "output arguments" : {
    "title": "Output arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to",
                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to.\n"
            ,
                "default": "$id.$key.output.output"
            }
    

        ,
                "tab": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format",
                "help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format.\n"
            ,
                "default": "False"
            }
    

        ,
                "bed_out": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format",
                "help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format.\n"
            ,
                "default": "False"
            }
    

        ,
                "name": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature",
                "help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature.\n"
            ,
                "default": "False"
            }
    

        ,
                "name_only": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature",
                "help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature.\n"
            ,
                "default": "False"
            }
    

        ,
                "split": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED",
                "help_text": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED.\n"
            ,
                "default": "False"
            }
    

        ,
                "full_header": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use full fasta header",
                "help_text": "Type: `boolean_true`, default: `false`. Use full fasta header. By default, only the word before the first space or tab is used.\n"
            ,
                "default": "False"
            }
    

}
},
    
    
    "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/input arguments"
    },

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

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

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