else {
//valid paramters for this command
- string Array[] = {"fasta","name", "group", "align" };
+ string Array[] = {"fasta","name", "group", "alignreport" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- alignfile = validParameter.validFile(parameters, "align", true);
+ alignfile = validParameter.validFile(parameters, "alignreport", true);
if (alignfile == "not open") { abort = true; }
else if (alignfile == "not found") { alignfile = ""; }
void ListSeqsCommand::help(){
try {
mothurOut("The list.seqs command reads a fasta, name, group or alignreport file and outputs a .accnos file containing sequence names.\n");
- mothurOut("The list.seqs command parameters are fasta, name, group and align. You must provide one of these parameters.\n");
+ mothurOut("The list.seqs command parameters are fasta, name, group and alignreport. You must provide one of these parameters.\n");
mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");