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