1 #ifndef Mothur_listotucommand_h
2 #define Mothur_listotucommand_h
8 // Created by Sarah Westcott on 5/15/12.
9 // Copyright (c) 2012 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "sharedrabundvector.h"
16 /**************************************************************************************************/
18 class ListOtuLabelsCommand : public Command {
20 ListOtuLabelsCommand(string);
21 ListOtuLabelsCommand();
22 ~ListOtuLabelsCommand(){}
24 vector<string> setParameters();
25 string getCommandName() { return "list.otulabels"; }
26 string getCommandCategory() { return "OTU-Based Approaches"; }
27 //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/List.otulabels"; }
32 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."; }
35 void help() { m->mothurOut(getHelpString()); }
39 string outputDir, sharedfile, relabundfile, label, inputFileName, format;
40 vector<string> outputNames;
41 vector<string> Groups;
44 int createList(vector<SharedRAbundFloatVector*>&);
45 int createList(vector<SharedRAbundVector*>&);
49 /**************************************************************************************************/