//**********************************************************************************************************************
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); }
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;