// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
-#include "GetCoreMicroBiomeCommand.h"
+#include "getcoremicrobiomecommand.h"
//**********************************************************************************************************************
vector<string> GetCoreMicroBiomeCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pabund("abundance", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter psamples("samples", "Number", "", "-1", "", "", "",false,false); parameters.push_back(psamples);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pabund("abundance", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psamples("samples", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(psamples);
+ 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); }
}
}
//**********************************************************************************************************************
+string GetCoreMicroBiomeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "coremicrobiome") { pattern = "[filename],[tag],core.microbiome"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["coremicrobiom"] = tempOutNames;
+ outputTypes["coremicrobiome"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
}
}
-
+ vector<string> tempOutNames;
+ outputTypes["coremicrobiome"] = tempOutNames;
+
//check for parameters
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiom";
- outputNames.push_back(outputFileName); outputTypes["coremicrobiom"].push_back(outputFileName);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[tag]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("coremicrobiome", variables);
+ outputNames.push_back(outputFileName); outputTypes["coremicrobiome"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
if (m->control_pressed) { return 0; }
if ((samples != -1) || (abund != -1)) {
- string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomlist";
- outputNames.push_back(outputFileName2); outputTypes["coremicrobiom"].push_back(outputFileName2);
+ string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomelist";
+ outputNames.push_back(outputFileName2); outputTypes["coremicrobiome"].push_back(outputFileName2);
ofstream out2;
m->openOutputFile(outputFileName2, out2);