List of usage examples for org.apache.commons.cli OptionBuilder hasArg
public static OptionBuilder hasArg(boolean hasArg)
hasArg is true. From source file:org.mitre.ccv.mapred.CompleteCompositionVectors.java
/** * * The JSO data will be the same as {@link org.mitre.ccv.CompleteMatrix#jsonCompleteMatrix}, but the features * will be in a different order. This version, by default sorts, only by entropy values, whereas the * ccv in-memory version sorts by the k-mer natural order (i.e., lexigraphic). * @param argv// www . j av a 2 s . c o m * @return * @throws java.lang.Exception */ @Override @SuppressWarnings("static-access") // For OptionBuilder public int run(String[] argv) throws Exception { JobConf conf = new JobConf(getConf()); String cli_title = "CompleteCompositionVectorHadoop"; int start = CalculateKmerCounts.DEFAULT_START; int end = CalculateKmerCounts.DEFAULT_END; int topkmers = 0; String input = null; String output = null; String vectorJsonOutput = null; //String kmerJsonOutput = null; boolean cleanLogs = false; /** create the Options */ Options options = new Options(); /** Hadoop Options */ options.addOption( OptionBuilder.withArgName("number").hasArg(true).withDescription("number of maps").create("m")); options.addOption( OptionBuilder.withArgName("number").hasArg(true).withDescription("number of reducers").create("r")); // org.hadoop.util.GenericOptionsParser should captures this, but it doesn't options.addOption(OptionBuilder.withArgName("property=value").hasArg(true).withValueSeparator() .withDescription("use value for given property").create("D")); /** CompleteCompositionVector Options */ options.addOption(OptionBuilder.withArgName("number").hasArg(true) .withDescription("number of top k-mers to use in calculations").create("topKmers")); options.addOption(OptionBuilder.withArgName("start").hasArg(true).withDescription("starting length of tile") .create("start")); options.addOption(OptionBuilder.withArgName("end").hasArg(true).withDescription("ending length of title") .create("end")); options.addOption(OptionBuilder.hasArg(true).withArgName("file") .withDescription("JSON file to write out k-mers to").create("kmersfile")); options.addOption(OptionBuilder.hasArg(true).withArgName("file") .withDescription("JSON file to write out feature vectors to " + "(Overrides kmersout, only one file will be written).") .create("vectorsfile")); options.addOption(OptionBuilder.withArgName("number").hasArg(true) .withDescription("What preference to use: 0-min 1-median 2-avg(min,med): default is median") .create("prefval")); options.addOption(OptionBuilder.withArgName("help").hasArg(false).withDescription("print this message") .create("help")); // automatically generate the help statement HelpFormatter formatter = new HelpFormatter(); //GenericOptionsParser gop = new GenericOptionsParser(conf, options, argv); GenericOptionsParser gop = new GenericOptionsParser(conf, argv); String[] remaining_args = gop.getRemainingArgs(); // create the parser CommandLineParser parser = new GnuParser(); //CommandLine line = gop.getCommandLine(); String[] other_args = new String[] {}; try { CommandLine line = parser.parse(options, remaining_args); other_args = line.getArgs(); // Make sure there is a parameter left. if (other_args.length == 0) { System.out.println(cli_title); System.out.println("Missing input path!"); formatter.printHelp("hccv [options] <input> [<output>] ", options); GenericOptionsParser.printGenericCommandUsage(System.out); return -1; } Option[] opts = line.getOptions(); if (line.hasOption("help")) { System.out.println(cli_title); formatter.printHelp("hccv [options] <input> [<output>] ", options); GenericOptionsParser.printGenericCommandUsage(System.out); return -1; } // could also use line.iterator() for (Option opt : opts) { if (opt.getOpt().equals("m")) { conf.setNumMapTasks(Integer.parseInt(opt.getValue())); } if (opt.getOpt().equals("r")) { conf.setNumReduceTasks(Integer.parseInt(opt.getValue())); } if (opt.getOpt().equals("D")) { // We can have multiple properties we want to set String[] properties = opt.getValues(); for (String property : properties) { String[] keyval = property.split("="); conf.set(keyval[0], keyval[1]); } } if (opt.getOpt().equals("start")) { start = Integer.parseInt(opt.getValue()); } if (opt.getOpt().equals("end")) { end = Integer.parseInt(opt.getValue()); } if (opt.getOpt().equals("topKmers")) { topkmers = Integer.parseInt(opt.getValue()); } if (opt.getOpt().equals("vectorsfile")) { vectorJsonOutput = opt.getValue(); } } } catch (ParseException e) { LOG.warn("options parsing faild: " + e.getMessage()); System.out.println(cli_title); formatter.printHelp("hccv [options] <input> [<output>] ", options); GenericOptionsParser.printGenericCommandUsage(System.out); } if (start <= 2) { throw new IllegalArgumentException("Value of 'start' argument must be larger than 2"); } input = other_args[0]; if (other_args.length < 2) { output = input + "_" + FileUtils.getSimpleDate(); } else { output = other_args[2]; } /** * Check output path. Either needs to exist as a directory or not exist */ Path outputPath = new Path(output); FileSystem fs = outputPath.getFileSystem(conf); if (!fs.exists(outputPath)) { fs.mkdirs(outputPath); } else if (fs.exists(outputPath) || !fs.getFileStatus(outputPath).isDir()) { LOG.fatal(String.format("Output directory %s already exists", outputPath.makeQualified(fs))); throw new FileAlreadyExistsException( String.format("Output directory %s already exists", outputPath.makeQualified(fs))); } String outputDir = output + Path.SEPARATOR; int res; /** * Zero, CalculateCompositionVectors */ LOG.info("Starting CalculateCompositionVectors Map-Reduce job"); CalculateCompositionVectors cv = new CalculateCompositionVectors(); res = cv.initJob(conf, start, end, input, outputDir + COMPOSITION_VECTORS, cleanLogs); if (res != 0) { LOG.info("CalculateCompositionVectors returned non-zero result!"); return res; } // We can stop now or continue to reduce dimensionallity using RRE or other means /** * First, CalculateKmerCounts */ LOG.info("Starting CalculateKmerCounts Map-Reduce job"); // FastMap option for CalculateKmers!?! CalculateKmerCounts ckc = new CalculateKmerCounts(); res = ckc.initJob(conf, start, end, input, outputDir + KMER_COUNTS); if (res != 0) { LOG.fatal("CalculateKmerCounts returned non-zero result!"); return res; } /** * Second, TotalSequenceLength */ LOG.info("Starting TotalSequenceLength Map-Reduce job"); TotalSequenceLength tsl = new TotalSequenceLength(); res = tsl.initJob(conf, input, outputDir + TOTAL_LENGTH, cleanLogs); if (res != 0) { LOG.fatal("TotalSequenceLength returned non-zero result!"); return res; } int length = tsl.getCount(conf, outputDir + TOTAL_LENGTH); if (length < 3) { LOG.fatal("TotalSequenceLength returned a total sequence length of less than 3."); return -1; } else { LOG.info(String.format("TotalSequenceLength returned a total sequence length of %d.", length)); } /** * Third, CalculateKmerProbabilities */ LOG.info("Starting CalculateKmerProbabilities Map-Reduce job"); CalculateKmerProbabilities ckp = new CalculateKmerProbabilities(); res = ckp.initJob(conf, start, end, length, outputDir + KMER_COUNTS, outputDir + KMER_PROBABILITIES, cleanLogs); if (res != 0) { LOG.fatal("CalculateKmerProbabilities returned non-zero result!"); return res; } /** * Fourth, InvertKmerProbabilities */ LOG.info("Starting InvertKmerProbabilities Map-Reduce job"); InvertKmerProbabilities ikp = new InvertKmerProbabilities(); res = ikp.initJob(conf, outputDir + KMER_PROBABILITIES, outputDir + INVERTED_KMER_PROBABILITIES, cleanLogs); if (res != 0) { LOG.fatal("InvertKmerProbabilities returned non-zero result!"); return res; } /** * Fifth, CalculateKmerPiValues */ LOG.info("Starting CalculateKmerPiValues Map-Reduce job"); CalculateKmerPiValues kpv = new CalculateKmerPiValues(); res = kpv.initJob(conf, start, end, outputDir + INVERTED_KMER_PROBABILITIES, outputDir + KMER_PI_VALUES, cleanLogs); if (res != 0) { LOG.fatal("CalculateKmerPiValues returned non-zero result!"); return res; } /** * Sixth,CalculateKmerRevisedRelativeEntropy */ LOG.info("Starting CalculateKmerRevisedRelativeEntropy Map-Reduce job"); CalculateKmerRevisedRelativeEntropy krre = new CalculateKmerRevisedRelativeEntropy(); res = krre.initJob(conf, outputDir + KMER_PI_VALUES, outputDir + COMPOSITION_VECTORS, outputDir + ENTROPY_VALUES, cleanLogs); if (res != 0) { LOG.fatal("CalculateKmerRevisedRelativeEntropy returned non-zero result!"); return res; } /** * Seventh, SortKmerRevisedRelativeEntropies */ SortKmerRevisedRelativeEntropies srre = new SortKmerRevisedRelativeEntropies(); res = srre.initJob(conf, outputDir + ENTROPY_VALUES, outputDir + SORTED_ENTROPY_VALUES, cleanLogs); if (res != 0) { LOG.fatal("SortKmerRevisedRelativeEntropies returned non-zero result!"); return res; } /** * Eigth, GenerateFeatureVectors * * Generate a flatten list to add to the cache to be distributed to the map-tasks. */ Path listOutputPath = new Path(outputDir + Integer.toString(topkmers) + KMER_ENTROPY_SET); LOG.info(String.format("Loading %d sorted k-mers from %s to %s", topkmers, outputDir + SORTED_ENTROPY_VALUES, listOutputPath.toString())); int num = CompleteCompositionVectorUtils.flattenKmerEntropySequenceFile(conf, topkmers, outputDir + SORTED_ENTROPY_VALUES, listOutputPath.toString(), cleanLogs); if (num != topkmers) { LOG.fatal(String.format("Requested %d k-mers, but got %d. Using %d", topkmers, num, num)); topkmers = num; } GenerateFeatureVectors fv = new GenerateFeatureVectors(); res = fv.initJob(conf, listOutputPath.toString(), topkmers, outputDir + COMPOSITION_VECTORS, outputDir + FEATURE_VECTORS, cleanLogs); if (res != 0) { LOG.fatal("GenerateFeatureVectors returned non-zero result!"); return res; } /** * Save feature vectors, features (k-mers), and properties to a JSON file. * * The data will be the same as {@link org.mitre.ccv.CompleteMatrix#jsonCompleteMatrix}, but the features * will be in a different order. This version, by default sorts, only by entropy values, whereas the * ccv in-memory version sorts by the k-mer natural order (i.e., lexigraphic). */ if (vectorJsonOutput != null && vectorJsonOutput.length() > 0) { LOG.info("Writing features out to " + vectorJsonOutput); CompleteCompositionVectorUtils.featureVectors2Json(conf, start, end, topkmers, outputDir + SORTED_ENTROPY_VALUES, outputDir + FEATURE_VECTORS, vectorJsonOutput); } LOG.info("All done generating complete composition vectors and feature vectors."); return res; }
From source file:org.nuunframework.cli.NuunCliPlugin.java
private Option createOptionFromField(Field field) { Option option = null;/* w w w .j ava 2s .co m*/ // Cli Option Builder is completly static :-/ // so we synchronized it ... synchronized (OptionBuilder.class) { // reset the builder creating a dummy option OptionBuilder.withLongOpt("dummy"); OptionBuilder.create(); // NuunOption nuunOption = field.getAnnotation(NuunOption.class); if (nuunOption == null) { for (Annotation anno : field.getAnnotations()) { if (AssertUtils.hasAnnotationDeep(anno.annotationType(), NuunOption.class)) { nuunOption = AssertUtils.annotationProxyOf(NuunOption.class, anno); break; } } } // longopt if (!Strings.isNullOrEmpty(nuunOption.longOpt())) { OptionBuilder.withLongOpt(nuunOption.longOpt()); } // description if (!Strings.isNullOrEmpty(nuunOption.description())) { OptionBuilder.withDescription(nuunOption.description()); } // required OptionBuilder.isRequired((nuunOption.required())); // arg OptionBuilder.hasArg((nuunOption.arg())); // args if (nuunOption.args()) { if (nuunOption.numArgs() > 0) { OptionBuilder.hasArgs(nuunOption.numArgs()); } else { OptionBuilder.hasArgs(); } } // is optional if (nuunOption.optionalArg()) { OptionBuilder.hasOptionalArg(); } // nuun OptionBuilder.withValueSeparator(nuunOption.valueSeparator()); // opt if (!Strings.isNullOrEmpty(nuunOption.opt())) { option = OptionBuilder.create(nuunOption.opt()); } else { option = OptionBuilder.create(); } } return option; }
From source file:org.openmainframe.ade.main.ControlDB.java
@Override protected void parseArgs(String[] args) throws AdeException { final Option helpOpt = new Option("h", "help", false, "Print help message and exit"); final Option forceOpt = new Option("f", "force", false, "Force operation. Do not prompt for confirmation"); OptionBuilder.withLongOpt("create"); OptionBuilder.hasArg(false); OptionBuilder.isRequired(false);/*from w w w . j a v a 2 s . com*/ OptionBuilder.withDescription("Create Ade DB tables"); final Option createOpt = OptionBuilder.create('c'); OptionBuilder.withLongOpt("drop"); OptionBuilder.hasArg(false); OptionBuilder.isRequired(false); OptionBuilder.withDescription("Drops all Ade DB tables, and clears the data store dictionaries"); final Option deleteOpt = OptionBuilder.create('d'); OptionBuilder.withLongOpt("reset"); OptionBuilder.hasArg(false); OptionBuilder.isRequired(false); OptionBuilder.withDescription("Clears all Ade DB tables content"); final Option resetOpt = OptionBuilder.create('r'); OptionBuilder.withLongOpt("query"); OptionBuilder.hasArg(); OptionBuilder.withArgName("SQL query string"); OptionBuilder.isRequired(false); OptionBuilder.withDescription("Performs the input query"); final Option queryOpt = OptionBuilder.create('q'); final OptionGroup actionGroupOpt = new OptionGroup().addOption(createOpt).addOption(deleteOpt) .addOption(resetOpt).addOption(queryOpt); actionGroupOpt.setRequired(true); final Options options = new Options(); options.addOption(helpOpt); options.addOption(forceOpt); options.addOptionGroup(actionGroupOpt); final CommandLineParser parser = new GnuParser(); CommandLine line = null; try { // parse the command line arguments line = parser.parse(options, args); } catch (MissingOptionException exp) { logger.error("Command line parsing failed.", exp); new HelpFormatter().printHelp(ControlDB.class.getName(), options); System.exit(0); } catch (ParseException exp) { // oops, something went wrong logger.error("Parsing failed. Reason: " + exp.getMessage()); throw new AdeUsageException("Argument Parsing failed", exp); } if (line.hasOption('h')) { new HelpFormatter().printHelp(getClass().getSimpleName(), options); closeAll(); System.exit(0); } if (line.hasOption('f')) { m_forceOp = true; } if (line.hasOption('c')) { m_op = ControlDBOperator.Create; } else if (line.hasOption('d')) { m_op = ControlDBOperator.Drop; } else if (line.hasOption('r')) { m_op = ControlDBOperator.Reset; } else if (line.hasOption('q')) { m_op = ControlDBOperator.Query; m_args = new String[] { line.getOptionValue('q') }; } }
From source file:org.semanticscience.narf.graphs.main.CycleExtractor.java
@SuppressWarnings("static-access") private static Options createOptions() { Options o = new Options(); OptionBuilder.withArgName("/path/to/input/dir"); Option inputPDBDir = OptionBuilder.hasArg(true) .withDescription("The directory where your input PDB files are located").create("inputPDBDir"); Option inputSeqFile = OptionBuilder.hasArg(true) .withDescription("The path to the file of one aptamer sequence per line").create("inputSeqFile"); Option outputDir = OptionBuilder.withArgName("/path/to/output/dir").hasArg(true) .withDescription("The directory where the cycle output will be stored").create("outputDir"); Option outputFormat = OptionBuilder.withArgName("outputFormat").hasArg(true) .withDescription("The output format for the cycles (RDF|tsv)").isRequired().create("outputFormat"); o.addOption(inputSeqFile);// w w w .ja va 2 s . c o m o.addOption(outputFormat); o.addOption(inputPDBDir); o.addOption(outputDir); return o; }
From source file:org.semanticscience.PDBAptamerRetriever.main.RetrieveAptamers.java
@SuppressWarnings("static-access") private static Options createOptions() { Options o = new Options(); // help option Option help = new Option("help", false, "Print this message"); Option getAll = OptionBuilder.hasArg(false).withDescription( "use this flag if you wish to download all rna and dna containing pdb structures both x-ray and nmr") .create("getall"); Option expMethod = OptionBuilder.withArgName("X-RAY").hasArg(true) .withDescription("Enter an expeirmental method. Valid options are X-RAY, NMR or all").create("em"); Option moleculeType = OptionBuilder.withArgName("RNA").hasArg(true) .withDescription("Enter a molecule type. Valid options are DNA, RNA, BOTH, ALLDNA or ALLRNA") .create("mt"); Option outputFastaDir = OptionBuilder.withArgName("/path/to/local/dir").hasArg(true) .withDescription("The directory where you wish to save your FASTA files").create("fastaDir"); Option concatenateFASTA = OptionBuilder.hasArg(false).withDescription( "Add this parameter if you want all of your FASTA files to be downloaded into a single file") .create("cf"); Option outputPDBDir = OptionBuilder.withArgName("/path/to/local/dir").hasArg(true) .withDescription("The directory where you wish to save your PDB files").create("pdbDir"); Option outputPDBMLDir = OptionBuilder.withArgName("/path/to/loca/pdbml/dir").hasArg(true) .withDescription("The directory where you wish to save your PDBML files").create("pdbmlDir"); Option ligandReport = OptionBuilder.hasArg(false) .withDescription("Add this parameter to create a ligand report").create("lr"); Option ligandFreqs = OptionBuilder.hasArg(false) .withDescription("Add this parameter to compute ligand counts").create("lf"); Option click = OptionBuilder.withArgName("/path/to/click/outputDir").hasArg(true).withDescription( "Add this parameter to run Click on all PDB files. Specify where to store the output of Click") .create("click"); Option needle = OptionBuilder.withArgName("/path/to/needle/outputDir").hasArg(true) .withDescription("Add this parameter to run EMBOSS's needle program on the downloaded fasta files") .create("needle"); Option gapOpen = OptionBuilder.withArgName("Gap open penalty").hasArg(true) .withDescription("Add this parameter if you are running Needle").create("gapOpen"); Option gapExtend = OptionBuilder.withArgName("Gap extend penalty").hasArg(true) .withDescription("Add this parameter if you are running Needle").create("gapExtend"); o.addOption(getAll);/*from ww w.ja v a 2 s.c o m*/ o.addOption(outputPDBMLDir); o.addOption(gapExtend); o.addOption(gapOpen); o.addOption(help); o.addOption(expMethod); o.addOption(moleculeType); o.addOption(outputFastaDir); o.addOption(concatenateFASTA); o.addOption(outputPDBDir); o.addOption(ligandReport); o.addOption(ligandFreqs); o.addOption(click); o.addOption(needle); return o; }
From source file:org.servalproject.maps.dataman.DataManCli.java
private static Options createOptions() { Options options = new Options(); // path to the input file OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the input file"); OptionBuilder.isRequired(true);/*from w w w. j a v a2 s .co m*/ options.addOption(OptionBuilder.create("input")); // path to the output file OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the output file"); OptionBuilder.isRequired(true); options.addOption(OptionBuilder.create("output")); // task to undertake OptionBuilder.withArgName("text"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("manipulation task to undertake"); OptionBuilder.isRequired(true); options.addOption(OptionBuilder.create("task")); // style information OptionBuilder.withArgName("text"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("style definition information"); OptionBuilder.isRequired(false); options.addOption(OptionBuilder.create("style")); // verbose output or not options.addOption(new Option("verbose", "use verbose output")); return options; }
From source file:org.servalproject.maps.indexgenerator.MapIndexGenerator.java
private static Options createOptions() { Options options = new Options(); OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the input directory"); OptionBuilder.isRequired(true);//from ww w . j a va2s . co m options.addOption(OptionBuilder.create("input")); OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the output file"); OptionBuilder.isRequired(true); options.addOption(OptionBuilder.create("output")); OptionBuilder.withArgName("text"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("output format type"); OptionBuilder.isRequired(true); options.addOption(OptionBuilder.create("format")); return options; }
From source file:org.servalproject.maps.mapfiletester.MapFileTester.java
private static Options createOptions() { Options options = new Options(); OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the input file / directory"); OptionBuilder.isRequired(true);//from w w w.ja va 2 s . c o m options.addOption(OptionBuilder.create("input")); return options; }
From source file:org.servalproject.maps.osmbboxsplit.OsmBBoxSplit.java
private static Options createOptions() { Options options = new Options(); OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the input file / directory"); OptionBuilder.isRequired(true);//w ww .j a va2 s .com options.addOption(OptionBuilder.create("input")); OptionBuilder.withArgName("int"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("minimum size of file in MB to split (Default: " + MIN_FILE_SIZE + " MB)"); OptionBuilder.isRequired(false); options.addOption(OptionBuilder.create("minsize")); OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the ignore list file"); OptionBuilder.isRequired(false); options.addOption(OptionBuilder.create("ignore")); OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the output directory"); OptionBuilder.isRequired(false); options.addOption(OptionBuilder.create("output")); OptionBuilder.withArgName("path"); OptionBuilder.hasArg(true); OptionBuilder.withDescription("path to the osmosis script template"); OptionBuilder.isRequired(false); options.addOption(OptionBuilder.create("template")); return options; }
From source file:org.structnetalign.CLI.java
private static Options getOptions() { Options options = new Options(); options.addOption(OptionBuilder.hasArg(true) .withDescription(//from w ww. j a v a2 s . co m "The number of cores to use. Defaults to the number of available processors minus one.") .isRequired(false).create("cores")); options.addOption(OptionBuilder.hasArg(true).withDescription( "The directory containing cached PDB files. Defaults to the AtomCache default, which is probably in your system's temporary directory (e.g. /tmp). It is okay if this is an empty directory, but the directory must exist. You should set up a PDB cache path if you plan to run " + PROGRAM_NAME + " multiple times.") .isRequired(false).create("pdb_dir")); options.addOption(OptionBuilder.hasArg(true).withDescription( "The maximum search depth for traversal during crossing. If a vertex v shares an interaction edge x with vertex s, vertex v shares an interaction edge y with vertex t, and there is no path from u to t and no path from v to s, then x will be updated by y if and only if u and v are seperated by no more than xi homology edges (inclusive), AND s and t are seperated by no more than xi homology edges. Defaults to " + PipelineManager.XI + ". See paper for more details.") .isRequired(false).create("xi")); options.addOption(OptionBuilder.hasArg(true).withDescription( "A threshold probability prior for running the crossing process. Prior to crossing, any homology edge with probability less than tau will be removed. Defaults to " + PipelineManager.TAU + ".") .isRequired(false).create("tau")); options.addOption(OptionBuilder.hasArg(true).withDescription( "A threshold probability prior for running the merging process. Prior to merging, any homology edge with probability less than zeta will be removed. Note that this is performed after a similar process for tau, so zeta should be no greater than tau. Defaults to " + PipelineManager.ZETA + ".") .isRequired(false).create("zeta")); options.addOption(OptionBuilder.hasArg(false).withDescription( "If set, generates an HTML report page with accompanying graph visualizations in the specified directory.") .isRequired(false).create("report")); options.addOption( OptionBuilder.hasArg(false).withDescription("Do not run the vertex degeneracy removal process.") .isRequired(false).create("no_merge")); options.addOption(OptionBuilder.hasArg(false).withDescription("Do not run the probability update process.") .isRequired(false).create("no_cross")); options.addOption(OptionBuilder.hasArg(true).withDescription("Required. The input PSI-MI25 XML file.") .isRequired(true).create("input")); options.addOption(OptionBuilder.hasArg(true).withDescription("Required. The output PSI-MI25 XML file.") .isRequired(true).create("output")); // options.addOption(OptionBuilder.hasArg(true) // .withDescription("The name of the PSI-MI25 confidence short label to use to give the initial weighting (probability) of an interaction as input to " + CLI.PROGRAM_NAME + ". Defaults to " + GraphInteractionAdaptor.INITIAL_CONFIDENCE_LABEL).isRequired(false) // .create("input_conf")); // options.addOption(OptionBuilder.hasArg(true) // .withDescription("The default weighting (probability) of an interaction if the interaction does not have a weight described by input_conf. Defaults to " + GraphInteractionAdaptor.DEFAULT_PROBABILITY).isRequired(false) // .create("default_weight")); // options.addOption(OptionBuilder.hasArg(true) // .withDescription("The name of the PSI-MI25 confidence short label to use to describe the certainty of an interaction as determined by " + CLI.PROGRAM_NAME + ". Defaults to " + GraphInteractionAdaptor.CONFIDENCE_SHORT_LABEL).isRequired(false) // .create("output_conf_label")); // options.addOption(OptionBuilder.hasArg(true) // .withDescription("The name of the PSI-MI25 confidence full name to use to describe certainty of an interaction as determined by " + CLI.PROGRAM_NAME + ". Defaults to " + GraphInteractionAdaptor.CONFIDENCE_FULL_NAME).isRequired(false) // .create("output_conf_name")); options.addOption(OptionBuilder.hasArg(false).withDescription("Output a GraphML file for each step.") .isRequired(false).create("write_steps")); options.addOption(OptionBuilder.hasArg(true).withDescription( "Skip the weighting process and use the specified GraphML file to indicate homology instead.") .isRequired(false).create("graphml_homology")); return options; }