added name option to trim.seqs

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 8775d95abab9a4577aaad0f29feec2d15bc39694..0e500d4982d372c95436b99e1ead81cb3c02a9c5 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -43,7 +43,7 @@ string ChopSeqsCommand::getHelpString(){
                helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
                helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
                helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -73,6 +73,7 @@ ChopSeqsCommand::ChopSeqsCommand(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();