help.append(" specified suffix.\n");
help.append("\n");
help.append("\n");
cl.addOption("-h",helpFlag,"Dumps the help message.");
cl.addOption("-o",ofn,"Output file name.");
cl.addOption("-workspace", workspace, "The workspace prefix");
cl.addOption("-indir",inDir,"The input directory");
cl.addOption("-of",outDir,"The output directory");
cl.addOption("-r",recursiveFlag,"Recurses through all subdirectories.");
cl.addOption("-skip",skip,"Skips the specified directory.");