//**********************************************************************************************************************
vector<string> PipelineCommand::setParameters(){
try {
- CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(psff);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(poligos);
- CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(palign);
- CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pchimera);
- CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pclassify);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(ptaxonomy);
- CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none",false,false); parameters.push_back(ppipeline);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(poligos);
+ CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(palign);
+ CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(pchimera);
+ CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(pclassify);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none","",false,false,true); parameters.push_back(ppipeline);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ 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 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
if (pipeFilename != "") {
abort = readUsersPipeline();
sffFile = validParameter.validFile(parameters, "sff", true);
if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
else if (sffFile == "not open") { sffFile = ""; abort = true; }
+ else { m->setSFFFile(sffFile); }
oligosFile = validParameter.validFile(parameters, "oligos", true);
if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }