m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine();
abort = true;
}
- }
+ }else { m->setPhylipFile(phylipfile); }
//check for required parameters
groupfile = validParameter.validFile(parameters, "group", true);
m->mothurOut("You must provide a group file."); m->mothurOutEndLine();
abort = true;
}
- }
+ }else { m->setGroupFile(groupfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){