{
    "parameters": [
        {
            "name": "bam",
            "label": "BAM file format flag",
            "usage": "Hlatyping will extract the reads and remap.",
            "type": "boolean",
            "render": "check-box",
            "default_value": false,
            "group": "input"
        },
        {
            "name": "singleEnd",
            "label": "Sequencing strategy",
            "usage": "Flag if input data is of type singleEnd.",
            "type": "boolean",
            "render": "check-box",
            "default_value": false,
            "group": "input"
        },
        {
            "name": "seqtype",
            "label": "Sequence type",
            "usage": "Tells hlatyping if input is of type DNA or RNA.",
            "type": "string",
            "render": "radio-button",
            "choices": ["dna", "rna"],
            "default_value": "dna",
            "group": "input"
        },
        {
            "name": "solver",
            "label": "IP solver alghorithm",
            "usage": "Selects an IP solver alghorithm for hlatyping.",
            "type": "string",
            "render": "radio-button",
            "choices": ["glpk", "cbc"],
            "default_value": "glpk",
            "group": "prediction"
        },
        {
            "name": "enumerations",
            "label": "Number of OptiType enumerations",
            "usage": "Shows additional n-1 suboptimal solutions from OptiType.",
            "type": "integer",
            "render": "range",
            "choices": [1,150],
            "default_value": 1,
            "group": "prediction"
        },
        {
            "name": "beta",
            "label": "Weight for homozygosity accounting",
            "usage": "Shows additional n-1 suboptimal solutions from OptiType-",
            "type": "decimal",
            "render": "range",
            "choices": [0.0, 0.1],
            "default_value": 0.009,
            "group": "prediction"
        },
        {
            "name": "prefix",
            "label": "Output file prefix.",
            "usage": "Adds a string prefix to the output files.",
            "type": "string",
            "render": "textfield",
            "default_value": "hla_run",
            "pattern": ".*",
            "group": "prediction"
        },
        {
            "name": "reads",
            "label": "Mapped or unmapped reads",
            "usage": "HLA typing workflow input data.",
            "type": "string",
            "render": "file",
            "default_value": "path/to/reads.fastq.gz",
            "pattern": ".*(\\.fastq$|\\.fastq\\.gz$|\\.bam$)",
            "group": "input"
        },
        {
            "name": "index",
            "label": "Reference index URI",
            "usage": "Yara HLA dna reference index location.",
            "type": "string",
            "render": "file",
            "default_value": "$baseDir/data/indices/yara/hla_reference_dna",
            "pattern": ".*",
            "group": "input"
        }
        
    ]
}
