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[mothur.git] / pipelinepdscommand.h

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
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+++ b/pipelinepdscommand.h
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+#ifndef PIPELINEPDSCOMMAND_H
+#define PIPELINEPDSCOMMAND_H
+
+/*
+ *  pipelinepdscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/5/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "commandfactory.hpp"
+
+/****************************************************/
+
+class PipelineCommand : public Command {
+       
+public:
+       PipelineCommand(string);
+       PipelineCommand() { abort = true; calledHelp = true; setParameters(); }
+       ~PipelineCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "pipeline.pds";        }
+       string getCommandCategory()             { return "Hidden";                      }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Pipeline.pds"; }
+       string getDescription()         { return "pat's pipeline"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       bool abort;
+       CommandFactory* cFactory;
+       vector<string> outputNames;
+       vector<string> commands;
+       string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
+       int processors;
+       
+       bool readUsersPipeline();
+       int runUsersPipeline();
+       void createPatsPipeline();
+       bool parseCommand(string, string&, string&);
+       bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
+       bool fillInMothurMade(string&, map<string, vector<string> >&);
+};
+
+/****************************************************/
+
+#endif
+