1 #ifndef GETGROUPSCOMMAND_H
2 #define GETGROUPSCOMMAND_H
8 * Created by westcott on 11/10/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
17 class GetGroupsCommand : public Command {
21 GetGroupsCommand(string);
25 vector<string> setParameters();
26 string getCommandName() { return "get.groups"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
32 string getDescription() { return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
36 void help() { m->mothurOut(getHelpString()); }
41 map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
42 //then the other files need to change the unique name in their file to match.
43 //only add the names that need to be changed to keep the map search quick
44 string accnosfile, countfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
46 vector<string> outputNames, Groups;