//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
- if (treefile == "not open") { abort = true; }
+ if (treefile == "not open") { treefile = ""; abort = true; }
else if (treefile == "not found") {
//if there is a current design file, use it
treefile = m->getTreeFile();
else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
}
if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
}
}