Merged in Nathan's changes for CMD_Bio Comamand line pramaters

Author: StevenAWhite

projects/cmd_bio/README.md

@@ -12,9 +12,9 @@ This project is a command line implementation of BioGears for processing Scenari
 
 **GENSTATES**: Generate Stabalized Patient States for all Patients
 
-**VALIDATE** Run one ore more validate senarios arguments include drug,patient,system,validation, or all.
+**VALIDATE** Run one ore more validate senarios arguments include drug,patient,system or all. Where `VALIDATE all` is the same as providing the following `VALIDATE drug patient system VERIFY`
 
-**VERIFRY**: Run all verifications and validations senarios mentioned above
+**VERIFY**: Run Verification.config
 
 **THREADS**: Takes and Integer to control the number of threads the pool will run when running multiple scnearios. 
 

projects/cmd_bio/src/cmd_bio_main.cpp

@@ -90,9 +90,6 @@ int main(int argc, char** argv)
   }
 
   if (args.Option("VERIFY")) {
-    run_patient_validation = true;
-    run_drug_validation = true;
-    run_system_validation = true;
     run_verification = true;
   }
 #ifdef CMD_BIO_SUPPORT_CIRCUIT_TEST
@@ -122,12 +119,10 @@ int main(int argc, char** argv)
         run_drug_validation = true;
       } else if (test == "system") {
         run_system_validation = true;
-      } else if (test == "validation") {
-        run_verification = true;
       } else if (test == "all") {
         run_patient_validation = run_drug_validation = run_system_validation = run_verification = true;
       } else {
-        std::cout << "Warrning: No Validation known as " << test << "exists.\n";
+         std::cout << "Warning: No Validation known as " << test << "exists.\n";
       }
     }
   }