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);
23 PipelineCommand() { abort = true; calledHelp = true; setParameters(); }
26 vector<string> setParameters();
27 string getCommandName() { return "pipeline.pds"; }
28 string getCommandCategory() { return "Hidden"; }
29 string getHelpString();
32 void help() { m->mothurOut(getHelpString()); }
36 CommandFactory* cFactory;
37 vector<string> outputNames;
38 vector<string> commands;
39 string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
42 bool readUsersPipeline();
43 int runUsersPipeline();
44 void createPatsPipeline();
45 bool parseCommand(string, string&, string&);
46 bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
47 bool fillInMothurMade(string&, map<string, vector<string> >&);
50 /****************************************************/