pipelinepdscommand.h

   1 #ifndef PIPELINEPDSCOMMAND_H
   2 #define PIPELINEPDSCOMMAND_H
   3
   4 /*
   5  *  pipelinepdscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 10/5/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "commandfactory.hpp"
  16
  17 /****************************************************/
  18
  19 class PipelineCommand : public Command {
  20
  21 public:
  22         PipelineCommand(string);
  23         PipelineCommand() { abort = true; calledHelp = true; setParameters(); }
  24         ~PipelineCommand(){}
  25
  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"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36         bool abort;
  37         CommandFactory* cFactory;
  38         vector<string> outputNames;
  39         vector<string> commands;
  40         string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
  41         int processors;
  42
  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> >&);
  49 };
  50
  51 /****************************************************/
  52
  53 #endif
  54