X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makefastqcommand.h;h=e3e0b70b087b17e5d6299052cb06567e9b7c9f69;hp=fd893ad590f2f8ed8590b4741a8a11e8ec0db484;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=c67cf4168e1a124088b6f017946f0aa1fbdf1301

diff --git a/makefastqcommand.h b/makefastqcommand.h
index fd893ad..e3e0b70 100644
--- a/makefastqcommand.h
+++ b/makefastqcommand.h
@@ -20,19 +20,26 @@ public:
 	MakeFastQCommand(string);	
 	MakeFastQCommand();
 	~MakeFastQCommand(){}
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "make.fastq";				}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
+	string getDescription()		{ return "creates a fastq file from a fasta and quality file"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
 	
-	string fastafile, qualfile, outputDir;
+	string fastafile, qualfile, outputDir, format;
 	bool abort;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	string convertQual(vector<int>);