if (randomtree == "") {
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (randomtree == "") {
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
else if (treefile == "not found") { //if there is a current design file, use it
treefile = m->getTreeFile();
if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
else if (treefile == "not found") { //if there is a current design file, use it
treefile = m->getTreeFile();
if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);