Command line help should automatically show available options for parameters that are enums.

[tfenne]

Command line help should automatically show available options for parameters that are enums.

[nh13]

For java enums, it works. For scala enums, see #40. See --log-level below:

java -jar target/scala-2.11/dagr-0.1.0-SNAPSHOT.jar -h
USAGE: Dagr [Dagr arguments] [pipeline name] [pipeline arguments]
Version:0.1.0-SNAPSHOT

Dagr Optional Arguments:
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-h [true|false], --help[=true|false]
                              Display the help message.  [Default: false].
--config=Path                 Load in a custom configuration into Dagr.  See https://github.com/typesafehub/config for
                              details on the file format.
--version[=true|false]        Display the version number for this tool.  [Default: false].
--script-dir=Path             Overrides the default scripts directory in the configuration file.
--log-dir=Path                Overrides default log directory in the configuration file.
-l LogLevel, --log-level=LogLevel
                              Set the logging level.  [Default: Info]. Options: Debug, Info, Warning, Error, Fatal.
--scripts=Path                Dagr scala scripts to compile and add to the list of programs.
--cores=Double                Set the number of cores available to dagr.
--memory=String               Set the memory available to dagr.
--report=Path                 Write an execution report to this file, otherwise write to the stdout

USAGE: Dagr [pipeline] [arguments]
Version:0.1.0-SNAPSHOT
Available Sub-Commands:
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Pipelines:                                      Various pipeline programs.                   
    CreateUnmappedBamFromFastqPipeline           Create Unmapped Bam From Fastq Pipeline.
    DnaResequencingFromFastqPipeline             Dna Resequencing from Fastq Pipeline.
    DnaResequencingFromUnmappedBamPipeline       Dna Resequencing From Unmapped BAM Pipeline.
    DownsampleAndCallSomaticVariants             Downsamples a Tumor BAM to various coverage levels and calls mutations in it.
    ExamplePipeline                              Example FASTQ to BAM pipeline.
    GermlineVariantCallingPipeline               Calls germline variants in a single sample and then hard filters them.
    SomaticVariantCallingPipeline                Calls somatic variants in a single sample [pair] and then filters them.
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