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();
30 string getCitation() { return "http://www.mothur.org/wiki/Pipeline.pds"; }
33 void help() { m->mothurOut(getHelpString()); }
37 CommandFactory* cFactory;
38 vector<string> outputNames;
39 vector<string> commands;
40 string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
43 bool readUsersPipeline();
44 int runUsersPipeline();
45 void createPatsPipeline();
46 bool parseCommand(string, string&, string&);
47 bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
48 bool fillInMothurMade(string&, map<string, vector<string> >&);
51 /****************************************************/