X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pipelinepdscommand.h;fp=pipelinepdscommand.h;h=8a8a195eef38c9787332c2b029c889f693c55639;hp=0000000000000000000000000000000000000000;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2

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() {}
+	~PipelineCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; } //empty
+	int execute();
+	void help();
+	
+private:
+	bool abort;
+	CommandFactory* cFactory;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
+	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
+