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 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"; }
36 void help() { m->mothurOut(getHelpString()); }
40 CommandFactory* cFactory;
41 vector<string> outputNames;
42 vector<string> commands;
43 string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
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> >&);
54 /****************************************************/