//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
else if (listfile == "not found") {
listfile = m->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
else if (listfile == "not found") {
listfile = m->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
outputTypes["shared"].push_back(filename);
filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
outputTypes["shared"].push_back(filename);
//clears file before we start to write to it below
for (int i=0; i<Groups.size(); i++) {
remove((fileroot + Groups[i] + ".rabund").c_str());
//clears file before we start to write to it below
for (int i=0; i<Groups.size(); i++) {
remove((fileroot + Groups[i] + ".rabund").c_str());