X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=86046b64375ebd151c27e5909c0efdc9d0149bbf;hb=cc19310422f125d6628980bd1148e1e816792382;hp=5f5235647d28168d4ca187189d5911266a24c71a;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 5f52356..86046b6 100644
--- 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();
@@ -137,6 +138,10 @@ int GetCurrentCommand::execute(){
 					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") {