kotlin docopt wrapper example

doctopt_with_wrapper.kts

#!/usr/bin/env kscript

//DEPS com.offbytwo:docopt:0.6.0.20150202,log4j:log4j:1.2.14,com.github.holgerbrandl:kscript:1.2.2-SNAPSHOT

//import org.docopt.Docopt
import java.util.*
import kscript.util.DocOpt

//val args = arrayOf("hg19", "/some/where/N.bam", "/some/where/aRG.bam", "/some/where/bRG.bam")

val usage = """
Use this cool tool to do cool stuff
Usage: cooltool.kts [options] <igenome> <fastq_files>...

Options:
 --gtf <gtfFile>     Custom gtf file instead of igenome bundled copy
 --pc-only           Use protein coding genes only for mapping and quantification
"""

val doArgs = DocOpt(args, usage)

println("Hello from Kotlin!")
println("Parsed script arguments are: \n" + doArgs)