//********************************************************************************************************************** vector<string> ClusterCommand::setParameters(){ try { CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list",false,false,true); parameters.push_back(pphylip); CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname); CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount); CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list",false,false,true); parameters.push_back(pcolumn); CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff); CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision); CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false,true); parameters.push_back(pmethod); CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund); CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming); CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim); CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); //CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust); 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); } return myArray; } catch(exception& e) { m->errorOut(e, "ClusterCommand", "setParameters"); exit(1); } }
// Test Change. //********************************************************************************************************************** vector<string> NewCommand::setParameters(){ try { //eaxamples of each type of parameter. more info on the types of parameters can be found in commandparameter.h CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors); //files that have dependancies CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","outputType",false,false); parameters.push_back(pphylip); CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","outputType",false,false); parameters.push_back(pname); CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","outputType",false,false); parameters.push_back(pcolumn); //files that do not have dependancies - fasta is set to not be required whereas shared is set to be required CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","outputType",false,false); parameters.push_back(pfasta); CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared); CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); //choose more than one multiple options CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "","",true,false); parameters.push_back(pcalc); //choose only one multiple options CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "","",false,false); parameters.push_back(pdistance); CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming); //every command must have inputdir and outputdir. This allows mothur users to redirect input and output files. CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed); 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); } return myArray; } catch(exception& e) { m->errorOut(e, "NewCommand", "setParameters"); exit(1); } }