vector<string> setParameters();
string getCommandName() { return "make.biom"; }
string getCommandCategory() { return "General"; }
+
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, groups, outputDir, format, label;
- vector<string> outputNames, Groups;
+ string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
+ vector<string> outputNames, Groups, sampleMetadata;
set<string> labels;
bool abort, allLines;
int getBiom(vector<SharedRAbundVector*>&);
vector<string> getMetaData(vector<SharedRAbundVector*>&);
vector<string> parseTax(string tax, vector<string>& scores);
+ int getSampleMetaData(vector<SharedRAbundVector*>&);
};