1 #ifndef Mothur_makebiomcommand_h
2 #define Mothur_makebiomcommand_h
8 // Created by Sarah Westcott on 4/16/12.
9 // Copyright (c) 2012 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "sharedrabundvector.h"
15 #include "inputdata.h"
18 class MakeBiomCommand : public Command {
21 MakeBiomCommand(string);
25 vector<string> setParameters();
26 string getCommandName() { return "make.biom"; }
27 string getCommandCategory() { return "General"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
32 string getDescription() { return "creates a biom file"; }
35 void help() { m->mothurOut(getHelpString()); }
39 string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
40 vector<string> outputNames, Groups, sampleMetadata;
45 int getBiom(vector<SharedRAbundVector*>&);
46 vector<string> getMetaData(vector<SharedRAbundVector*>&);
47 vector<string> parseTax(string tax, vector<string>& scores);
48 int getSampleMetaData(vector<SharedRAbundVector*>&);