changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 94a60d4db9ff198423a401b74cbb7e78e9c010a5..aac16371f1251fc4c7b78639427f95896aa4c223 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -114,7 +114,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 
 void ClassifyOtuCommand::help(){
        try {
-               m->mothurOut("The classify.otu command parameters are list, taxonomy, name, cutoff, and label.  The taxonomy and list parameters are required.\n");
+               m->mothurOut("The classify.otu command parameters are list, taxonomy, name, cutoff, label and probs.  The taxonomy and list parameters are required.\n");
                m->mothurOut("The name parameter allows you add a names file with your taxonomy file.\n");
                m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
                m->mothurOut("The default value for label is all labels in your inputfile.\n");