{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "rseqc_inner_distance",
"description": "Calculate inner distance between read pairs.\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input_file": {
                "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"
            
            }
    

        ,
                "sample_size": {
                "type":
                "integer",
                "description": "Type: `integer`, example: `1000000`. Numer of reads sampled from SAM/BAM file, default = 1000000",
                "help_text": "Type: `integer`, example: `1000000`. Numer of reads sampled from SAM/BAM file, default = 1000000."
            
            }
    

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

        ,
                "lower_bound": {
                "type":
                "integer",
                "description": "Type: `integer`, example: `-250`. Lower bound of inner distance (bp)",
                "help_text": "Type: `integer`, example: `-250`. Lower bound of inner distance (bp). This option is used for ploting histograme, default=-250."
            
            }
    

        ,
                "upper_bound": {
                "type":
                "integer",
                "description": "Type: `integer`, example: `250`. Upper bound of inner distance (bp)",
                "help_text": "Type: `integer`, example: `250`. Upper bound of inner distance (bp). This option is used for ploting histograme, default=250."
            
            }
    

        ,
                "step": {
                "type":
                "integer",
                "description": "Type: `integer`, example: `5`. Step size (bp) of histograme",
                "help_text": "Type: `integer`, example: `5`. Step size (bp) of histograme. This option is used for plotting histogram, default=5."
            
            }
    

}
},
    
    
    "output" : {
    "title": "Output",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output_prefix": {
                "type":
                "string",
                "description": "Type: `string`, required. Rrefix of output files",
                "help_text": "Type: `string`, required. Rrefix of output files."
            
            }
    

        ,
                "output_stats": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads",
                "help_text": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads"
            ,
                "default":"$id.$key.output_stats.output_stats"
            }
    

        ,
                "output_dist": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads"
            ,
                "default":"$id.$key.output_dist.output_dist"
            }
    

        ,
                "output_freq": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads"
            ,
                "default":"$id.$key.output_freq.output_freq"
            }
    

        ,
                "output_plot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads"
            ,
                "default":"$id.$key.output_plot.output_plot"
            }
    

        ,
                "output_plot_r": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads",
                "help_text": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads"
            ,
                "default":"$id.$key.output_plot_r.output_plot_r"
            }
    

}
},
    
    
    "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"
    }
]
}
