X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mantelcommand.cpp;h=409eae414779acb412abec7aa295b61e82cd0e16;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=c41cde34e92374d4c21a57f51636d2729d464d13;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index c41cde3..409eae4 100644
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -41,7 +41,7 @@ string MantelCommand::getHelpString(){
 		helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n";
 		helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n";
 		helpString += "The mantel command outputs a .mantel file.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -69,6 +69,7 @@ MantelCommand::MantelCommand(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 {
 			vector<string> myArray = setParameters();
@@ -124,7 +125,7 @@ MantelCommand::MantelCommand(string option)  {
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found"){	method = "pearson";		}
 			
 			string temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters);
+			m->mothurConvert(temp, iters);
 			
 			if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
 		}