1 #ifndef GETLINEAGECOMMAND_H
2 #define GETLINEAGECOMMAND_H
8 * Created by westcott on 9/24/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
15 class GetLineageCommand : public Command {
19 GetLineageCommand(string);
21 ~GetLineageCommand(){};
22 vector<string> getRequiredParameters();
23 vector<string> getValidParameters();
24 vector<string> getRequiredFiles();
25 map<string, vector<string> > getOutputFiles() { return outputTypes; }
31 vector<string> outputNames;
32 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
34 map<string, vector<string> > outputTypes;
42 string removeConfidences(string);