initial commit of FLASh app controller
test of second commit of FLASh app controller
added all paramters
removed MixedParameter
indentation fixes
started convenience functions
added to convenience functions. started to add class methods
added synonyms dict and getHelp method
removed extra '}'
changed getHelp doc string'}'
added a few private methods
removed some import statements
edited '-d' value param
changed miseq suggested max overlap param
updated code in '_get_result_paths'
explicitly check for absolute file paths in 'default_assemble'
changed working_dir to WorkingDir in 'default_assemble'
started test cases for flash.py
commented out the default Value settings for ValuedParameters
added 'test_base_command' method and started to code basic 'setUP'