X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getcurrentcommand.cpp;h=d74786ce1eaaa8767164a0fbd670d06843388b44;hp=86046b64375ebd151c27e5909c0efdc9d0149bbf;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=f687723a8357916e86a05116978e6869b039ce36

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 86046b6..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);		}
@@ -142,6 +142,8 @@ int GetCurrentCommand::execute(){
 					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") {