- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter psvg("svg", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psvg);
- CommandParameter pincrement("increment", "Number", "", "10", "", "", "",false,false); parameters.push_back(pincrement);
- CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
- 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 ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
+ CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
+ CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
+ 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);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+