changed dups parameter to dereplicate in chimera.uchime.

[mothur.git] / getcurrentcommand.cpp

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 2f67123a88c9795c362fac6cc4a428fc8e961d46..86046b64375ebd151c27e5909c0efdc9d0149bbf 100644 (file)
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -59,6 +59,7 @@ GetCurrentCommand::GetCurrentCommand(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();
@@ -135,6 +136,14 @@ int GetCurrentCommand::execute(){
                                        m->setAccnosFile("");
                                }else if (types[i] == "taxonomy") {
                                        m->setTaxonomyFile("");
+                               }else if (types[i] == "flow") {
+                                       m->setFlowFile("");
+                }else if (types[i] == "biom") {
+                                       m->setBiomFile("");
+                }else if (types[i] == "count") {
+                                       m->setCountTableFile("");
+                               }else if (types[i] == "processors") {
+                                       m->setProcessors("1");
                                }else if (types[i] == "all") {
                                        m->clearCurrentFiles();
                                }else {
@@ -143,8 +152,10 @@ int GetCurrentCommand::execute(){
                        }
                }
                
-               m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
-               m->printCurrentFiles();
+               if (m->hasCurrentFiles()) {
+                       m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+                       m->printCurrentFiles();
+               }
                
                return 0;       
        }