X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitabundcommand.cpp;h=ba59dfe66e1b333f88317542e3a17844ac6d558e;hb=75962c819c16814e5c2340d99af1aa62e564dc20;hp=810b83915dadb9ed8863340dcfb27ac34e286dd8;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 810b839..ba59dfe 100644
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -48,7 +48,7 @@ string SplitAbundCommand::getHelpString(){
 		helpString += "If you want .abund and .rare files for all groups, set groups=all.  \n";
 		helpString += "The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n";
 		helpString += "Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\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) {
@@ -82,11 +82,9 @@ SplitAbundCommand::SplitAbundCommand(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","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string, string> parameters = parser.getParameters();