X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=86046b64375ebd151c27e5909c0efdc9d0149bbf;hb=b866e1519a60681527244036428104ad1cb90c93;hp=9289ba6da677a6e91f989a3b15c5f407d32ce3f8;hpb=82bf18e3ef0a52345519f91a682e64cc385b56bb;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 9289ba6..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();
@@ -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 {