added chimera.uchime

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 911e65fc9f8696834448ff9b3451b53e43f496b6..620de95c333cdee1360157f7aa7068f3ce1f1f62 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -15,6 +15,7 @@ vector<string> SeqSummaryCommand::setParameters(){
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -36,7 +37,7 @@ string SeqSummaryCommand::getHelpString(){
                helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n";
                helpString += "The summary.seqs command should be in the following format: \n";
                helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n";
-               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";     
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -66,6 +67,7 @@ SeqSummaryCommand::SeqSummaryCommand(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();