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);
}
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
}
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
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);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }