helpString += "The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n";
helpString += "Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n";
helpString += "The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
return helpString;
}
catch(exception& e) {
//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();
designfile = m->getDesignFile();
if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setDesignFile(designfile); }
//make sure the user has already run the read.otu command
sharedfile = validParameter.validFile(parameters, "shared", true);
sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setSharedFile(sharedfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }