added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / getcurrentcommand.cpp

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 9289ba6da677a6e91f989a3b15c5f407d32ce3f8..ca832314d66dbe371e314db292ab6f441d2ee351 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 +136,12 @@ 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] == "processors") {
+                                       m->setProcessors("1");
                                }else if (types[i] == "all") {
                                        m->clearCurrentFiles();
                                }else {