#include "command.hpp"
#include "sharedrabundvector.h"
+#include "listvector.hpp"
/**************************************************************************************************/
string getCommandName() { return "list.otulabels"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
- string getHelpString();
+
+ string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/List.otulabels"; }
- string getDescription() { return "lists otu labels from shared or relabund file. Can be used with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
+ string getDescription() { return "lists otu labels from shared or relabund file. Can be used by get.otulabels with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
- string outputDir, sharedfile, relabundfile, label, inputFileName, format;
+ string outputDir, sharedfile, relabundfile, label, inputFileName, format, listfile;
vector<string> outputNames;
vector<string> Groups;
set<string> labels;
int createList(vector<SharedRAbundFloatVector*>&);
int createList(vector<SharedRAbundVector*>&);
+ int createList(ListVector*&);
};