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));