//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
m->setTaxonomyFile("");
}else if (types[i] == "flow") {
m->setFlowFile("");
+ }else if (types[i] == "biom") {
+ m->setBiomFile("");
}else if (types[i] == "processors") {
m->setProcessors("1");
}else if (types[i] == "all") {