//**********************************************************************************************************************
vector<string> TrimFlowsCommand::setParameters(){
try {
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow",false,true,true); parameters.push_back(pflow);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow-file",false,true,true); parameters.push_back(pflow);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
if (type == "flow") { pattern = "[filename],[tag],flow"; }
else if (type == "fasta") { pattern = "[filename],flow.fasta"; }
- else if (type == "file") { pattern = "[filename],[tag],flow.files"; }
+ else if (type == "file") { pattern = "[filename],flow.files"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
if(allFiles){
set<string> namesAlreadyProcessed;
- variables["[tag]"] = "";
flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
output.close();
}
else{
- variables["[tag]"] = "";
flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);