
...
                    TavernaExtractor extractor = new TavernaExtractor(verbose);
                    extractor.setTavernaHome(Main.getTavernaHome(tavernaHome));
                    extractor.setArchimateOutputPath(Paths.get(archimateOutputPath));
                    extractor.setInputFileName(Paths.get(inputFileName));
                    extractor.setDotLocation(Paths.get(dotExeLocation));

                    if(parse.hasOption("a") && parse.getOptionValue("a") != null)
                        extractor.shouldAddDepJars(parse.getOptionValue("a"));

                    extractor.process(false); //false = local execution
                }

                // List all provenance entries OR Running DROID identification
                if (parse.hasOption("p")) {
...

        OptionBuilder.withDescription("verbose mode one");
        OptionBuilder.withLongOpt("verbose");
        options.addOption(OptionBuilder.create("v"));

        OptionBuilder.withDescription("detect and add taverna's jar dependencies");
        OptionBuilder.withArgName("\\path\\to\\taverna\\executable");
        OptionBuilder.hasArg();
        OptionBuilder.withLongOpt("add taverna dependencies");
        options.addOption(OptionBuilder.create("a"));

        return options;
    }

    private static Path getTavernaHome(String tavernaHome){


	a/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/Main.java		b/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/Main.java
	...		...
65	TavernaExtractor extractor = new TavernaExtractor(verbose);	65	TavernaExtractor extractor = new TavernaExtractor(verbose);
66	extractor.setTavernaHome(Main.getTavernaHome(tavernaHome));	66	extractor.setTavernaHome(Main.getTavernaHome(tavernaHome));
67	extractor.setArchimateOutputPath(Paths.get(archimateOutputPath));	67	extractor.setArchimateOutputPath(Paths.get(archimateOutputPath));
68	extractor.setInputFileName(Paths.get(inputFileName));	68	extractor.setInputFileName(Paths.get(inputFileName));
69	extractor.setDotLocation(Paths.get(dotExeLocation));	69	extractor.setDotLocation(Paths.get(dotExeLocation));
		70
		71	if(parse.hasOption("a") && parse.getOptionValue("a") != null)
		72	extractor.shouldAddDepJars(parse.getOptionValue("a"));
		73
70	extractor.process(false); //false = local execution	74	extractor.process(false); //false = local execution
71	}	75	}
72		76
73	// List all provenance entries OR Running DROID identification	77	// List all provenance entries OR Running DROID identification
74	if (parse.hasOption("p")) {	78	if (parse.hasOption("p")) {
	...		...
180		184
181	OptionBuilder.withDescription("verbose mode one");	185	OptionBuilder.withDescription("verbose mode one");
182	OptionBuilder.withLongOpt("verbose");	186	OptionBuilder.withLongOpt("verbose");
183	options.addOption(OptionBuilder.create("v"));	187	options.addOption(OptionBuilder.create("v"));
184		188
		189	OptionBuilder.withDescription("detect and add taverna's jar dependencies");
		190	OptionBuilder.withArgName("\\path\\to\\taverna\\executable");
		191	OptionBuilder.hasArg();
		192	OptionBuilder.withLongOpt("add taverna dependencies");
		193	options.addOption(OptionBuilder.create("a"));
		194
185	return options;	195	return options;
186	}	196	}
187		197
188	private static Path getTavernaHome(String tavernaHome){	198	private static Path getTavernaHome(String tavernaHome){
189		199