a0e8e6b7cdb37cf071a36fc0eeb3d78a879fb9a0,src/main/java/japsa/tools/bio/hts/VNTRLongReadsCmd.java,VNTRLongReadsCmd,VNTRLongReadsCmd,#,76

Before Change


				"Name of the output file, -  for stdout");
		addString("xafFile", null, "Name of the regions file in xaf",
				true);
		addInt("flanking", 30, "Size of the flanking regions");
		addInt("qual", 0, "Minimum quality");
		addInt("iteration", 1, "Number of iteration");
		addInt("nploidy",2,

After Change


		addString("xafFile", null, "Name of the regions file in xaf",
				true);
		
		CommandLine.Option flankingOpt =
		addInt("flanking", 30, "Size of the flanking regions");
		
		CommandLine.Option minQualOpt =
		addInt("qual", 0, "Minimum quality");
		
		addInt("iteration", 1, "Number of iteration");
		addInt("nploidy",2,
				"The ploidy of the genome 1 =  happloid, 2 = diploid. Currenly only support up to 2-ploidy");
		addString("prefix", "",
				"Prefix of temporary files, if not specified, will be automatically generated");

		///////////////Adding galaxy support/////////////
		flankingOpt.setGalaxySetting(new GalaxySetting("integer", null,false));
		minQualOpt.setGalaxySetting(new GalaxySetting("integer", null,false));
		xafFileOpt.setGalaxySetting(new GalaxySetting("data", "tabular",false));