5 // Created by SarahsWork on 5/28/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef Mothur_renameseqscommand_h
10 #define Mothur_renameseqscommand_h
12 #include "command.hpp"
14 class RenameSeqsCommand : public Command {
17 RenameSeqsCommand(string);
19 ~RenameSeqsCommand() {}
21 vector<string> setParameters();
22 string getCommandName() { return "rename.seqs"; }
23 string getCommandCategory() { return "Sequence Processing"; }
25 string getHelpString();
26 string getOutputPattern(string);
27 string getCitation() { return "http://www.mothur.org/wiki/Rename.seqs"; }
28 string getDescription() { return "rename sequences"; }
32 void help() { m->mothurOut(getHelpString()); }
37 string fastaFile, nameFile, groupfile, outputDir;
38 vector<string> outputNames;
41 map<string, string> nameMap;