string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
sffFile = validParameter.validFile(parameters, "sff", true);
if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
else if (sffFile == "not open") { sffFile = ""; abort = true; }
sffFile = validParameter.validFile(parameters, "sff", true);
if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
else if (sffFile == "not open") { sffFile = ""; abort = true; }
oligosFile = validParameter.validFile(parameters, "oligos", true);
if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
oligosFile = validParameter.validFile(parameters, "oligos", true);
if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }