1 #ifndef PIPELINEPDSCOMMAND_H
2 #define PIPELINEPDSCOMMAND_H
8 * Created by westcott on 10/5/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "commandfactory.hpp"
17 /****************************************************/
19 class PipelineCommand : public Command {
22 PipelineCommand(string);
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; } //empty
34 CommandFactory* cFactory;
35 vector<string> outputNames;
36 map<string, vector<string> > outputTypes;
37 vector<string> commands;
38 string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
41 bool readUsersPipeline();
42 int runUsersPipeline();
43 void createPatsPipeline();
44 bool parseCommand(string, string&, string&);
45 bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
46 bool fillInMothurMade(string&, map<string, vector<string> >&);
49 /****************************************************/