added citation function to commands

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index a70be07e955180d17208b47f50d92f82ba2fa438..eaf8cc206cebfe6eb1a60b40ff7042ede86ef6bd 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -54,7 +54,7 @@ string ClassifyOtuCommand::getHelpString(){
                helpString += "The probs parameter shuts off the outputting of the consensus confidence results. The default is true, meaning you want the confidence to be shown.\n";
                helpString += "The classify.otu command should be in the following format: classify.otu(taxonomy=yourTaxonomyFile, list=yourListFile, name=yourNamesFile, label=yourLabels).\n";
                helpString += "Example classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, label=0.10).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -87,7 +87,8 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                //allow user to run help
                if (option == "help") { 
                        help(); abort = true; calledHelp = true;
-               } else {
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;} 
+               else {
                        vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);