X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=d74786ce1eaaa8767164a0fbd670d06843388b44;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=5f5235647d28168d4ca187189d5911266a24c71a;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 5f52356..d74786c 100644
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -12,9 +12,9 @@
 //**********************************************************************************************************************
 vector<string> GetCurrentCommand::setParameters(){	
 	try {
-		CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -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 +138,12 @@ 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] == "summary") {
+					m->setSummaryFile("");
 				}else if (types[i] == "processors") {
 					m->setProcessors("1");
 				}else if (types[i] == "all") {