X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makebiomcommand.h;h=8f07c40d439529355af3fb3ee78e11b6b23aab7a;hp=ee9bd1c99cf415c93b57fc85087a06d870298115;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=5c5c0428f6d548c28a8b903ac80efed4f92d59db

diff --git a/makebiomcommand.h b/makebiomcommand.h
index ee9bd1c..8f07c40 100644
--- a/makebiomcommand.h
+++ b/makebiomcommand.h
@@ -25,8 +25,9 @@ public:
 	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"; }
     
@@ -35,16 +36,19 @@ public:
 	
 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();
 };