X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.h;h=8abe0ea7a439e99aae5be49dc5734516ce9bdab1;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=8a8a195eef38c9787332c2b029c889f693c55639;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
index 8a8a195..8abe0ea 100644
--- a/pipelinepdscommand.h
+++ b/pipelinepdscommand.h
@@ -20,20 +20,24 @@ 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 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;
-	map<string, vector<string> > outputTypes;
 	vector<string> commands;
 	string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
 	int processors;
@@ -43,7 +47,7 @@ private:
 	void createPatsPipeline();
 	bool parseCommand(string, string&, string&);
 	bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
-	bool fillInMothurMade(string&, map<string, vector<string> >);
+	bool fillInMothurMade(string&, map<string, vector<string> >&);
 };
 
 /****************************************************/