working on pam

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 97fcd1cce71290949fde06e96086ab0cc48db70b..9148576b9135826ffe33b084d833525af182bb5a 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -26,8 +26,12 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "libshuff";                            }
        string getCommandCategory()             { return "Hypothesis Testing";          }
-       string getHelpString(); 
        
+       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"; }
+
        int execute();
        void help() { m->mothurOut(getHelpString()); }