added parameter to chimera.uchime

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index cc4b69f27259fae22b74a17e0dd4826b476cce3f..4d71c07511d711ec10baad3b94ca724cbf1e320f 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -71,7 +71,7 @@ string SummaryCommand::getHelpString(){
                helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
                helpString += "If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n";
                helpString += "The label parameter is used to analyze specific labels in your input.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -102,6 +102,7 @@ SummaryCommand::SummaryCommand(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();
@@ -222,6 +223,11 @@ SummaryCommand::SummaryCommand(string option)  {
                                 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
                        }
                        m->splitAtDash(calc, Estimators);
+                       if (m->inUsersGroups("citation", Estimators)) { 
+                               ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+                               //remove citation from list of calcs
+                               for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+                       }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }