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;
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> >&);
};
/****************************************************/