X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makebiomcommand.h;h=1ff398518c850c0447ff58c904b1ceddf9b6c3d3;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=ee9bd1c99cf415c93b57fc85087a06d870298115;hpb=a9dbc22713bfc056a797361dd757b1a5c98e1c01;p=mothur.git

diff --git a/makebiomcommand.h b/makebiomcommand.h
index ee9bd1c..1ff3985 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"; }
     
@@ -35,14 +36,14 @@ public:
 	
 private:
     
-	string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
+	string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label, referenceTax;
 	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> getMetaData(vector<SharedRAbundVector*>&, vector<string>&);
     vector<string> parseTax(string tax, vector<string>& scores);
     int getSampleMetaData(vector<SharedRAbundVector*>&);
 };