#include "inputdata.h"
#include "sharedrabundvector.h"
-class GlobalData;
-
class MergeGroupsCommand : public Command {
public:
MergeGroupsCommand(string);
MergeGroupsCommand();
- ~MergeGroupsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~MergeGroupsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "merge.groups"; }
+ string getCommandCategory() { return "General"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
+ string getDescription() { return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
GroupMap* designMap;
vector<SharedRAbundVector*> lookup;
- map<string, vector<string> > outputTypes;
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used