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"
15 #include "listvector.hpp"
17 /**************************************************************************************************/
19 class ListOtuLabelsCommand : public Command {
21 ListOtuLabelsCommand(string);
22 ListOtuLabelsCommand();
23 ~ListOtuLabelsCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "list.otulabels"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
28 //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "http://www.mothur.org/wiki/List.otulabels"; }
33 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."; }
36 void help() { m->mothurOut(getHelpString()); }
40 string outputDir, sharedfile, relabundfile, label, inputFileName, format, listfile;
41 vector<string> outputNames;
42 vector<string> Groups;
45 int createList(vector<SharedRAbundFloatVector*>&);
46 int createList(vector<SharedRAbundVector*>&);
47 int createList(ListVector*&);
51 /**************************************************************************************************/