Merge pull request #18 from teharrison/master

updates and renaming
Merge pull request #19 from teharrison/master

added error message when invalid options combo used
take arguments from command line
Merge branch 'master' of github.com:MG-RAST/MG-RAST-Tools
return BIOM format
Merge pull request #20 from wgerlach/master

take arguments from command line
Adding Shock repo as submodule so we can use Shock libraries
Merge pull request #21 from jaredbischof/master

Adding Shock repo as submodule so we can use Shock libraries
readme update
Merge branch 'master' of github.com:MG-RAST/MG-RAST-Tools
add md5 to search list
added R stuff to tools