}else { m->setFastaFile(fastafile); }
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); }
}
string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
//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"){ outputDir = m->hasPath(fastafile); }
-
+
+ if (namefile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
catch(exception& e) {