{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "bedtools_bamtobed",
"description": "Converts BAM alignments to BED6 or BEDPE format.",
"type": "object",
"definitions": {

    
    
    "inputs" : {
    "title": "Inputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input": {
                "type":
                "string",
                "description": "Type: `file`, required. Input BAM file",
                "help_text": "Type: `file`, required. Input BAM file."
            
            }
    

}
},
    
    
    "outputs" : {
    "title": "Outputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.output.output`. Output BED file",
                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output BED file."
            ,
                "default": "$id.$key.output.output"
            }
    

}
},
    
    
    "options" : {
    "title": "Options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "bedpe": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Write BEDPE format",
                "help_text": "Type: `boolean_true`, default: `false`. Write BEDPE format. Requires BAM to be grouped or sorted by query.\n"
            ,
                "default": "False"
            }
    

        ,
                "mate1": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE \"block\"",
                "help_text": "Type: `boolean_true`, default: `false`. When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE \"block\".\n"
            ,
                "default": "False"
            }
    

        ,
                "bed12": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Write \"blocked\" BED format (aka \"BED12\")",
                "help_text": "Type: `boolean_true`, default: `false`. Write \"blocked\" BED format (aka \"BED12\"). Forces -split.\nSee http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1\n"
            ,
                "default": "False"
            }
    

        ,
                "split": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Report \"split\" BAM alignments as separate BED entries",
                "help_text": "Type: `boolean_true`, default: `false`. Report \"split\" BAM alignments as separate BED entries.\nSplits only on N CIGAR operations.\n"
            ,
                "default": "False"
            }
    

        ,
                "splitD": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Split alignments based on N and D CIGAR operators",
                "help_text": "Type: `boolean_true`, default: `false`. Split alignments based on N and D CIGAR operators.\nForces -split.\n"
            ,
                "default": "False"
            }
    

        ,
                "edit_distance": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use BAM edit distance (NM tag) for BED score",
                "help_text": "Type: `boolean_true`, default: `false`. Use BAM edit distance (NM tag) for BED score.\n- Default for BED is to use mapping quality.\n- Default for BEDPE is to use the minimum of\n  the two mapping qualities for the pair.\n- When -ed is used with -bedpe, the total edit\n  distance from the two mates is reported.\n"
            ,
                "default": "False"
            }
    

        ,
                "tag": {
                "type":
                "string",
                "description": "Type: `string`, example: `SM`. Use other NUMERIC BAM alignment tag for BED score",
                "help_text": "Type: `string`, example: `SM`. Use other NUMERIC BAM alignment tag for BED score.\nDefault for BED is to use mapping quality. Disallowed with BEDPE output.\n"
            
            }
    

        ,
                "color": {
                "type":
                "string",
                "description": "Type: `string`, example: `250,250,250`. An R,G,B string for the color used with BED12 format",
                "help_text": "Type: `string`, example: `250,250,250`. An R,G,B string for the color used with BED12 format.\nDefault is (255,0,0).\n"
            
            }
    

        ,
                "cigar": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Add the CIGAR string to the BED entry as a 7th column",
                "help_text": "Type: `boolean_true`, default: `false`. Add the CIGAR string to the BED entry as a 7th column.\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/inputs"
    },

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

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

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