vector<string> setParameters();
string getCommandName() { return "make.biom"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
string getDescription() { return "creates a biom file"; }
private:
- string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
+ string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label, referenceTax, picrustOtuFile;
vector<string> outputNames, Groups, sampleMetadata;
set<string> labels;
- bool abort, allLines;
+ bool abort, allLines, picrust;
int getBiom(vector<SharedRAbundVector*>&);
vector<string> getMetaData(vector<SharedRAbundVector*>&);
vector<string> parseTax(string tax, vector<string>& scores);
int getSampleMetaData(vector<SharedRAbundVector*>&);
+ //for picrust
+ int getGreenGenesOTUIDs(vector<SharedRAbundVector*>&, map<string, string>&);
+ map<string, string> readGGOtuMap();
};