//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
string temp;
else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (listFile == "not open") { abort = true; }
+ else { m->setListFile(listFile); }
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not found") { phylipfile = ""; }
else if (phylipfile == "not open") { abort = true; }
- else { distFile = phylipfile; format = "phylip"; }
+ else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not found") { columnfile = ""; }
else if (columnfile == "not open") { abort = true; }
- else { distFile = columnfile; format = "column"; }
+ else { distFile = columnfile; format = "column"; m->setColumnFile(columnfile); }
if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
//give priority to column, then phylip