X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pipelinepdscommand.h;h=22386bcc697c2e3c64767ad99dd9fafaaa5d206f;hp=a5061599472400895d1dfc1fac41320f7a880864;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=fc9bc621a09de13eb76ca4f5cee930b03de43dcd

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
index a506159..22386bc 100644
--- a/pipelinepdscommand.h
+++ b/pipelinepdscommand.h
@@ -20,20 +20,25 @@ 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();
+	PipelineCommand() { abort = true; calledHelp = true; setParameters(); }
+	~PipelineCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "pipeline.pds";	}
+	string getCommandCategory()		{ return "Hidden";			}
+	string getHelpString();	
+    string getOutputPattern(string) { return ""; }	
+	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"; }
+	string getDescription()		{ return "pat's pipeline"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 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;