Fixed some typos and added in functionality to automattically redirect stdout and stderr to python file object
Changed to use the ExtendedCommandLineApplication class
Fixed a bug where positional arguments were not cleared
The _positionals variable was a class variable and not an instance variable
Forgot to add in the WorkingDir parameter
Update the stderr and stdout file objects for reading and writing
changed around some logic so that the prependPositionals variable works properly
Added in a couple of convienence functions for printing the command and adding in positional arguments
Fixed the _get_result_paths method
The working directory is now taken into account when generating
the result paths
Update the pipeline to use phrap_pycogent