+//**********************************************************************************************************************
+vector<string> LibShuffCommand::getValidParameters(){
+ try {
+ string Array[] = {"iters","groups","step","form","cutoff","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+LibShuffCommand::LibShuffCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["coverage"] = tempOutNames;
+ outputTypes["libshuffsummary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> LibShuffCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> LibShuffCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"phylip","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getRequiredFiles");
+ exit(1);
+ }
+}