Exposed new command line arguments passed into the swift script.
The promised array append option appears to be unsupported. Moving to growing a string via a command line.
 Taking a new approach. The idea is to now construct the full Atlas command in python. This includes dummy variables for parallel parameters such as BAM file, sample name, and output name. This command is then passed in to the swift script, and the dummy variables are replaced with actual values using regular expressions. Note: we should test whether the regular expressions are actually implemented in Swift.
Command line construction within swift is working. Need to flesh out the parameter parsing in the python wrapper. Need to work out kinks in command execution in swift.
Swift submission is now verified.
Exposed additional atals parameters in python wrapper. Next we need to modify the XML wrapper to provide a galaxy interface to those parameters.
First pass at modifying the XML wrapper. This is as of yet untested.
fixed an unescaped char.
Removed unnecessary parameter manipulation in xml conditional.