//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
//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();
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);
else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
}
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 ((!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; }