if(option == "help") { help(); abort = true; }
else {
- if (option = "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
- else { command = option; }
+ if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
+ else {
+ //check for outputdir and inputdir parameters
+ int commaPos = option.find_first_of(',');
+
+ //if there is a comma then grab string up to that pos
+ if (commaPos != option.npos) {
+ option = option.substr(0, commaPos);
+ }
+
+ command = option;
+ }
}
}