+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::setParameters(){
+ try {
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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, "PhylotypeCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PhylotypeCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";
+ helpString += "The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n";
+ helpString += "The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n";
+ helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
+ helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
+ helpString += "The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n";
+ helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
+ helpString += "The phylotype command should be in the following format: \n";
+ helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
+ helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+ exit(1);
+ }
+}