ToolCommand

abstract def argsParser: AbstractOptParser[Args]

This is the parser object that will be tested.

abstract def descriptionText: String

Force description to be written for each tool.

abstract def emptyArgs: Args

Returns an empty/default args case class

abstract def exampleText: String

Force an example to be written for each tool

abstract def main(args: Array[String]): Unit

This is the main entry point of the tool

abstract def manualText: String

Force a manual to be written for each tool

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def aboutText: String

Universal text referring to BIOPET.

final def asInstanceOf[T0]: T0

def clone(): AnyRef

def cmdArrayToArgs(args: Array[String]): Args

Converts args to a Args case class

def contactText: String

Universal contact text

def contributingText: String

Universal contributing text

def documentationText: String

Universal text for pointing to the documentation.

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def example(args: String*): String

Convert and tests args

def finalize(): Unit

def generateDocumentation(outputDirectory: File, version: String, release: Boolean = false): Unit

Outputs markdown documentation for LAIKA processing.

def generateReadme(outputFile: File): Unit

Generates the README

final def getClass(): Class[_]

def hashCode(): Int

def installationText: String

Universal installation text

final def isInstanceOf[T0]: Boolean

def logger: Logger

def mainPageContents: List[(String, String)]

Which chapters should be on the tool documentation's main page

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def readmeContents: List[(String, String)]

Which chapters should be in the README

def sparkExample(args: String*): String

Convert and tests args

def sparkUnsafeExample(args: String*): String

Convert and *not* tests args

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

def toolName: String

This will return the name of the tool

def unsafeExample(args: String*): String

Convert and *not* tests args

def urlToolName: String

This is the tool name to be used in URL.

def usageText: String

Creates a html formatted usage string

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit