try {
CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
+ CommandParameter pmodnames("modifynames", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmodnames);
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);
helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
+ helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees. modifynames=F will leave sequence names as they are.\n";
helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n";
helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
else { debug = m->isTrue(temp); }
m->debug = debug;
+ bool nomod = false;
+ temp = validParameter.validFile(parameters, "modifynames", false);
+ if (temp == "not found") { modifyNames = true; nomod=true; }
+ else { modifyNames = m->isTrue(temp); }
+ m->modifyNames = modifyNames;
+
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;
+ if ((input == "") && (output == "") && (tempdefault == "") && nodebug && nomod) {
+ m->mothurOut("You must provide either an input, output, tempdefault, debug or modifynames for the set.outdir command."); m->mothurOutEndLine(); abort = true;
}else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; }
}
}