class ReadOtuCommand : public Command {
public:
ReadOtuCommand(string);
+ ReadOtuCommand();
~ReadOtuCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
InputData* input;
Command* shared;
GroupMap* groupMap;
- string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups;
- vector<string> Groups;
+ string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
+ vector<string> Groups, outputNames;
+ map<string, vector<string> > outputTypes;
bool abort, allLines;
set<string> labels; //holds labels to be used