- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "libshuff"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-6. \nSchloss PD, Larget BR, Handelsman J (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-92. \nhttp://www.mothur.org/wiki/Libshuff"; }
+ string getDescription() { return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }