X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyotucommand.cpp;h=eaf8cc206cebfe6eb1a60b40ff7042ede86ef6bd;hb=ec1b5bc7460ac8ad40f54f0729900d9ed98e7292;hp=a70be07e955180d17208b47f50d92f82ba2fa438;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index a70be07..eaf8cc2 100644
--- 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);