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 getOutputPattern(string) { return ""; }
  31         string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Pipeline.pds"; }
  32         string getDescription()         { return "pat's pipeline"; }
  33
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         bool abort;
  40         CommandFactory* cFactory;
  41         vector<string> outputNames;
  42         vector<string> commands;
  43         string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
  44         int processors;
  45
  46         bool readUsersPipeline();
  47         int runUsersPipeline();
  48         void createPatsPipeline();
  49         bool parseCommand(string, string&, string&);
  50         bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
  51         bool fillInMothurMade(string&, map<string, vector<string> >&);
  52 };
  53
  54 /****************************************************/
  55
  56 #endif
  57