Update REAMDE file so that it has the most updated version of the instructions for using the command line interface.
Fix code block formatting in the README file
Replace pre and code tags with backticks in the README file so that it is formatted fully in markdown
Remove redundant line from README file
Replace additional code tag with backtick in README file
Merge pull request #169 from dmcglinn/master

Add a command line usage section to the  README file