{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "rseqc_junctionsaturation",
"description": "Compare detected splice junctions to reference gene model.\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input": {
                "type":
                "string",
                "description": "Type: `file`, required. input alignment file in BAM or SAM format",
                "help_text": "Type: `file`, required. input alignment file in BAM or SAM format"
            
            }
    

        ,
                "refgene": {
                "type":
                "string",
                "description": "Type: `file`, required. Reference gene model in bed format",
                "help_text": "Type: `file`, required. Reference gene model in bed format"
            
            }
    

        ,
                "sampling_percentile_lower_bound": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `5`. Sampling starts from this percentile, must be an integer between 0 and 100, default =5",
                "help_text": "Type: `integer`, default: `5`. Sampling starts from this percentile, must be an integer between 0 and 100, default =5."
            ,
                "default":5
            }
    

        ,
                "sampling_percentile_upper_bound": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `100`. Sampling ends at this percentile, must be an integer between 0 and 100, default =5",
                "help_text": "Type: `integer`, default: `100`. Sampling ends at this percentile, must be an integer between 0 and 100, default =5."
            ,
                "default":100
            }
    

        ,
                "sampling_percentile_step": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `5`. Sampling frequency in %",
                "help_text": "Type: `integer`, default: `5`. Sampling frequency in %. Smaller value means more sampling times. Must be an integer between 0 and 100, default = 5."
            ,
                "default":5
            }
    

        ,
                "min_intron": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50",
                "help_text": "Type: `integer`, default: `50`. Minimum intron length (bp), default = 50."
            ,
                "default":50
            }
    

        ,
                "min_splice_read": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1",
                "help_text": "Type: `integer`, default: `1`. Minimum number of supporting reads to call a junction, default = 1."
            ,
                "default":1
            }
    

        ,
                "map_qual": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30",
                "help_text": "Type: `integer`, default: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30."
            ,
                "default":30
            }
    

}
},
    
    
    "output" : {
    "title": "Output",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output_plot_r": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate junction_saturation_plot plot",
                "help_text": "Type: `file`, default: `$id.$key.output_plot_r.r`. r script to generate junction_saturation_plot plot"
            ,
                "default":"$id.$key.output_plot_r.r"
            }
    

        ,
                "output_plot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_plot.pdf`. plot of junction saturation (pdf)",
                "help_text": "Type: `file`, default: `$id.$key.output_plot.pdf`. plot of junction saturation (pdf)"
            ,
                "default":"$id.$key.output_plot.pdf"
            }
    

}
},
    
    
    "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"
    },

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

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