ae45e41da0e37b567ade52401b3a7f207013b081,src/main/java/japsa/tools/bio/np/NanoporeReadFilterCmd.java,NanoporeReadFilterCmd,NanoporeReadFilterCmd,#,57

Before Change


		addDouble("qualMin", 0, "Minimum average quality");		
		addDouble("qualMax", 1000, "Maximum average quality");
		addBoolean("excl2D", false, "Exclude 2D reads");
		addBoolean("exclTemp", false, "Exclude template reads");
		addBoolean("exclComp", false, "Exclude complement reads");
		addString("format", "fastq", "Format of the output file");

After Change


		CommandLine.Option excl2DOpt =
				addBoolean("excl2D", false, "Exclude 2D reads");

		CommandLine.Option exclTempOpt =
				addBoolean("exclTemp", false, "Exclude template reads");

		CommandLine.Option exclCompOpt =
				addBoolean("exclComp", false, "Exclude complement reads");

		//CommandLine.Option formatOpt =
		addString("format", "fastq", "Format of the output file");

		addStdHelp();


		inputOpt.setGalaxySetting(new GalaxySetting("data", "fastqsanger",false));
		groupOpt.setGalaxySetting(new GalaxySetting("text", null, false));

		lenMinOpt.setGalaxySetting(new GalaxySetting("integer", null,false));
		//lenMaxOpt.setGalaxySetting(new GalaxySetting("integer", null,false));
		qualMinOpt.setGalaxySetting(new GalaxySetting("integer", null,false));
		//qualMaxOpt.setGalaxySetting(new GalaxySetting("integer", null,false));

		excl2DOpt.setGalaxySetting(new GalaxySetting("boolean", null,false));
		exclTempOpt.setGalaxySetting(new GalaxySetting("boolean", null,false));
		exclCompOpt.setGalaxySetting(new GalaxySetting("boolean", null,false));