X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=4536d9516688fe6db1d9c10e709e789c40abe93c;hb=b0997605981902442138b9309e9c43d95c3ba10a;hp=b0d12b87bc49f4d3b6e9cae63558ba622b199701;hpb=4f3d46bdb42c23468a534486fd105180b030fc65;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index b0d12b8..4536d95 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 vector<string> SetDirectoryCommand::setParameters(){	
 	try {
-		CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
-        CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug);
-		CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
-		CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
+        CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
+		CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput);
+		CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); parameters.push_back(poutput);
+		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);		}
@@ -92,6 +92,8 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
 			if (temp == "not found") {  debug = false;  nodebug=true; }
             else {  debug = m->isTrue(temp); }
             m->debug = debug;
+            
+            if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
 				
 			if ((input == "") && (output == "") && (tempdefault == "") && nodebug) {	
 				m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true;