temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
nseqs = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "4"; }
+ temp = validParameter.validFile(parameters, "permute", false);
+ if (temp == "not found"){ temp = "4"; }
+ else {
+ if ((temp == "1") || (temp == "2") || (temp == "3") || (temp == "4")) {}
+ else {
+ bool permTrue = m->isTrue(temp);
+ if (permTrue) { temp = "4"; }
+ else { }
+ }
+ }
m->mothurConvert(temp, perm);
if ((perm == 1) || (perm == 2) || (perm == 3) || (perm == 4)) { }
- else { m->mothurOut("[ERROR]: Not a valid permute value. Valid values are 1, 2, 3, and 4."); m->mothurOutEndLine(); abort = true; }
+ else { m->mothurOut("[ERROR]: Not a valid permute value. Valid values are 1, 2, 3, 4 and true."); m->mothurOutEndLine(); abort = true; }
temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; }
sharedOtus = m->isTrue(temp);