{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "dupradar",
"description": "Assessment of duplication rates in RNA-Seq datasets\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "id": {
                "type":
                "string",
                "description": "Type: `string`. Sample ID",
                "help_text": "Type: `string`. Sample ID"
            
            }
    

        ,
                "input": {
                "type":
                "string",
                "description": "Type: `file`, required. path to input alignment file in BAM format",
                "help_text": "Type: `file`, required. path to input alignment file in BAM format"
            
            }
    

        ,
                "gtf_annotation": {
                "type":
                "string",
                "description": "Type: `file`, required. path to GTF annotation file",
                "help_text": "Type: `file`, required. path to GTF annotation file."
            
            }
    

        ,
                "paired": {
                "type":
                "boolean",
                "description": "Type: `boolean`. add flag if input alignment file consists of paired reads",
                "help_text": "Type: `boolean`. add flag if input alignment file consists of paired reads"
            
            }
    

        ,
                "strandedness": {
                "type":
                "string",
                "description": "Type: `string`, choices: ``forward`, `reverse`, `unstranded``. strandedness of input bam file reads (forward, reverse or unstranded (default, applicable to paired reads))",
                "help_text": "Type: `string`, choices: ``forward`, `reverse`, `unstranded``. strandedness of input bam file reads (forward, reverse or unstranded (default, applicable to paired reads))",
                "enum": ["forward", "reverse", "unstranded"]
            
            
            }
    

}
},
    
    
    "output" : {
    "title": "Output",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output_dupmatrix": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts",
                "help_text": "Type: `file`, default: `$id.$key.output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts"
            ,
                "default": "$id.$key.output_dupmatrix.txt"
            }
    

        ,
                "output_dup_intercept_mqc": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar",
                "help_text": "Type: `file`, default: `$id.$key.output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar"
            ,
                "default": "$id.$key.output_dup_intercept_mqc.txt"
            }
    

        ,
                "output_duprate_exp_boxplot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot",
                "help_text": "Type: `file`, default: `$id.$key.output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot"
            ,
                "default": "$id.$key.output_duprate_exp_boxplot.pdf"
            }
    

        ,
                "output_duprate_exp_densplot": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts",
                "help_text": "Type: `file`, default: `$id.$key.output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts"
            ,
                "default": "$id.$key.output_duprate_exp_densplot.pdf"
            }
    

        ,
                "output_duprate_exp_denscurve_mqc": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_duprate_exp_denscurve_mqc.txt`. path to output file (pdf) of density curve of gene duplication multiqc",
                "help_text": "Type: `file`, default: `$id.$key.output_duprate_exp_denscurve_mqc.txt`. path to output file (pdf) of density curve of gene duplication multiqc"
            ,
                "default": "$id.$key.output_duprate_exp_denscurve_mqc.txt"
            }
    

        ,
                "output_expression_histogram": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram",
                "help_text": "Type: `file`, default: `$id.$key.output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram"
            ,
                "default": "$id.$key.output_expression_histogram.pdf"
            }
    

        ,
                "output_intercept_slope": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_intercept_slope.txt`. output file (txt) with progression of duplication rate value",
                "help_text": "Type: `file`, default: `$id.$key.output_intercept_slope.txt`. output file (txt) with progression of duplication rate value"
            ,
                "default": "$id.$key.output_intercept_slope.txt"
            }
    

}
},
    
    
    "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"
    }
]
}
