//**********************************************************************************************************************
vector<string> MakeGroupCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
+string MakeGroupCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "group") { pattern = "[filename],groups"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(){
try {
abort = true; calledHelp = true;
}
//prevent giantic file name
- if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
- else { filename += "groups"; }
+ map<string, string> variables;
+ variables["[filename]"] = filename;
+ if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; }
+ filename = getOutputFileName("group",variables);
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
out.close();
m->mothurOutEndLine();
- m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
+ m->mothurOut("Output File Names: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
m->mothurOutEndLine();
//set group file as new current groupfile