X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setlogfilecommand.cpp;h=576a37c11a26a656d34a9af69972dc4c3a329233;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=00e702c7b86d3d7bd16dfa5a162250f49402dae1;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 00e702c..576a37c 100644
--- a/setlogfilecommand.cpp
+++ b/setlogfilecommand.cpp
@@ -35,7 +35,7 @@ string SetLogFileCommand::getHelpString(){
 		helpString += "The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n";
 		helpString += "The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n";
 		helpString += "Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -51,11 +51,10 @@ SetLogFileCommand::SetLogFileCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
-			//valid paramters for this command
-			string Array[] =  {"name","append","outputdir","inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string, string> parameters = parser.getParameters();