//**********************************************************************************************************************
vector<string> MGClusterCommand::setParameters(){
try {
CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "",false,false); parameters.push_back(pmethod);
CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin);
CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge);
CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster);
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, "MGClusterCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
vector<string> FilterSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
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); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> SensSpecCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","sensspec",false,true,true); parameters.push_back(plist);
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pphylip);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pcolumn);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "","",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
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, "SensSpecCommand", "setParameters");
exit(1);
}
}
