X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefastqcommand.h;h=9119ebd50c4c9362e73a72902b888d4f1d06b887;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=fd893ad590f2f8ed8590b4741a8a11e8ec0db484;hpb=c67cf4168e1a124088b6f017946f0aa1fbdf1301;p=mothur.git

diff --git a/makefastqcommand.h b/makefastqcommand.h
index fd893ad..9119ebd 100644
--- a/makefastqcommand.h
+++ b/makefastqcommand.h
@@ -20,19 +20,25 @@ 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 getOutputFileNameTag(string, string);
+	string getHelpString();	
+	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;
 	bool abort;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	string convertQual(vector<int>);