- CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pquery);
- CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(preference);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(pqfile);
- CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(preport);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
- CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none","errorType",false,true,true); parameters.push_back(pquery);
+ CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(preference);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(pqfile);
+ CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(preport);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pignorechimeras);
+ CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter paligned("aligned", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(paligned);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);