vector<string> setParameters();
string getCommandName() { return "merge.groups"; }
string getCommandCategory() { return "General"; }
+ string getOutputFileNameTag(string, string);
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()); }
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
- string groups, label, outputDir, inputDir, designfile, sharedfile;
+ string groups, label, outputDir, inputDir, designfile, sharedfile, groupfile;
vector<string> Groups, outputNames;
int process(vector<SharedRAbundVector*>&, ofstream&);
+ int processSharedFile(GroupMap*&);
+ int processGroupFile(GroupMap*&);
};
#endif