CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc);
CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs);
+ CommandParameter psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus);
CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
perm = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; }
+ sharedOtus = m->isTrue(temp);
temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
m->mothurConvert(temp, fontsize);
//if the users entered no valid calculators don't execute command
if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; }
- venn = new Venn(outputDir, nseqs, inputfile, fontsize);
+ venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus);
input = new InputData(inputfile, format);
string lastLabel;