changed blastdb.cpp to no include sequence names in blast input filenames. modified...

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index e7d12969a73a1a2d6576593fc36ec8eb5a9b1d2a..c03fcc1ac133572fc7d821816edadc0b1fc32ecb 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -45,7 +45,7 @@ string PhylotypeCommand::getHelpString(){
                helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
                helpString += "The phylotype command should be in the following format: \n";
                helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
-               helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n";
+               helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -76,6 +76,7 @@ PhylotypeCommand::PhylotypeCommand(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();