List of usage examples for org.apache.commons.cli OptionBuilder withLongOpt
public static OptionBuilder withLongOpt(String newLongopt)
From source file:com.anjlab.sat3.Program.java
@SuppressWarnings("static-access") private static Options getCommandLineOptions() { Options options = new Options(); options.addOption(/*w w w . ja va 2 s .co m*/ OptionBuilder.withLongOpt("help").withDescription("Prints this help message.").create(HELP_OPTION)); options.addOption(OptionBuilder.withLongOpt("use-pretty-print") .withDescription("If specified, program will print detailed information about " + "formulas including triplet values." + "\nUseful when studying how algorithm works (especially if variables count less than 20)." + "\nDisabled by default.") .create(USE_PRETTY_PRINT_OPTION)); options.addOption(OptionBuilder.withLongOpt("disable-assertions") .withDescription( "Disables internal program self-check during execution. This may improve performance.") .create(DISABLE_ASSERTIONS_OPTION)); options.addOption(OptionBuilder.withLongOpt("use-abc-var-names") .withDescription("If specified, program will use ABC names for variables " + "(like 'a', 'b', ..., 'z' instead of 'x1', 'x2', etc.) during formula output." + "\nDisabled by default. Forced disabled if variables count more than 26.") .create(USE_ABC_VAR_NAMES_OPTION)); options.addOption(OptionBuilder.withLongOpt("hss-image-output").hasArg().withArgName("filename") .withDescription( "File name where visual representation of resulting basic graph will be written (only for SAT instances). Defaults to <input-file-name>-hss-0.png") .create(HSS_IMAGE_OUTPUT_FILENAME_OPTION)); options.addOption(OptionBuilder.withLongOpt("output").hasArg().withArgName("filename").withDescription( "File name where results of calculation will be written (time measurements and satisfying set for SAT instances). Defaults to <input-file-name>-results.txt") .create(RESULTS_OUTPUT_FILE_OPTION)); options.addOption(OptionBuilder.withLongOpt("evaluate-formula").hasArg().withArgName("filename") .withDescription("Evaluate formula using variable values from this file.").create(EVALUATE_OPTION)); options.addOption(OptionBuilder.withLongOpt("create-skt") .withDescription("Convert input formula to Romanov SKT file format.").create(CREATE_SKT_OPTION)); options.addOption(OptionBuilder.withLongOpt("find-hss-route").hasArg().withArgName("dirname") .withDescription("Find route in HSS from folder <dirname>").create(FIND_HSS_ROUTE_OPTION)); options.addOption(OptionBuilder.withLongOpt("generate-3sat-formula") .withDescription( "Generate 3-SAT formula from <input-file-name> and save it to <input-file-name>-3sat.cnf.") .create(GENERATE_3SAT_OPTION)); return options; }
From source file:com.aerospike.examples.timeseries.TimeSeriesManipulator.java
public static void main(String[] args) throws ParseException, FileNotFoundException, IOException, org.apache.commons.cli.ParseException, InterruptedException { try {/* w ww . jav a 2 s.co m*/ Options options = new Options(); options.addOption("h", "host", true, "Server hostname (default: localhost)"); options.addOption("p", "port", true, "Server port (default: 3000)"); options.addOption("t", "ticker", true, "Ticker (default: AAPL,IBM,ORCL,MSFT,CSCO)"); options.addOption("o", "op", true, "Load or Read Data (default: R)"); options.addOption("s", "start", true, "Start Date for Query (format: dd/MM/yyyy)"); options.addOption("e", "end", true, "End Date for Query (for,at: dd/MM/yyyy)"); options.addOption("d", "days", true, "Number of Days (default: from the stocktick.txt file)"); options.addOption(OptionBuilder.withLongOpt("help").create('l')); String header = "Options\n\n"; //String footer = "\nPlease report issues aveekshith@aerospike.com"; HelpFormatter formatter = new HelpFormatter(); CommandLineParser parser = new PosixParser(); CommandLine cl = parser.parse(options, args, false); String host = cl.getOptionValue("h", "127.0.0.1"); String portString = cl.getOptionValue("p", "3000"); String tickerList = cl.getOptionValue("t", "AAPL,IBM,ORCL,MSFT,CSCO"); String operation = cl.getOptionValue("o", "R"); String days = cl.getOptionValue("d"); DateOperator dateOperator = new DateOperator(); String prevDate, currentDate; if (days != null) prevDate = dateOperator.getPrevDate(days); else prevDate = dateOperator.getPrevDate("100"); currentDate = dateOperator.getCurrentDate(); String startDate = cl.getOptionValue("s", prevDate); String endDate = cl.getOptionValue("e", currentDate); if (cl.hasOption("l")) { formatter.printHelp("java -jar target/AeroTimeSeries-1.0.jar", header, options, null, true); System.exit(0); } else { int port = Integer.parseInt(portString); TimeSeriesManipulator ts = new TimeSeriesManipulator(host, port, tickerList, startDate, endDate, operation, days); ts.run(); } } catch (Exception ex) { System.out.println("Exception: " + ex.toString()); ex.printStackTrace(); } }
From source file:ca.uqac.info.trace.execution.BabelTrace.java
/** * Sets up the options for the command line parser * @return The options/*from w w w . j a v a 2s. c om*/ */ @SuppressWarnings("static-access") private static Options setupOptions() { Options options = new Options(); Option opt; opt = OptionBuilder.withLongOpt("run") .withDescription("Run the selected tool after conversion (default: no)").create("r"); options.addOption(opt); opt = OptionBuilder.withLongOpt("help").withDescription("Display command line usage").create("h"); options.addOption(opt); opt = OptionBuilder.withLongOpt("batch") .withDescription("Don't run the tool, but output the command line that would be used").create("b"); options.addOption(opt); opt = OptionBuilder.withLongOpt("trace").withArgName("filename").hasArg() .withDescription("Read trace from filename").create("t"); options.addOption(opt); opt = OptionBuilder.withLongOpt("formula").withArgName("filename").hasArg() .withDescription("Read formula from filename").create("f"); options.addOption(opt); opt = OptionBuilder.withLongOpt("convert").withArgName("toolname").hasArg() .withDescription("Convert to format of toolname").create("c"); options.addOption(opt); opt = OptionBuilder.withLongOpt("version").withDescription("Show version of BabelTrace").create(); options.addOption(opt); opt = OptionBuilder.withLongOpt("input-type").withArgName("type").hasArg() .withDescription("Trace input type").create("i"); options.addOption(opt); opt = OptionBuilder.withLongOpt("output-dir").withArgName("dir").hasArg() .withDescription("Write output files to dir").create("o"); options.addOption(opt); return options; }
From source file:com.flaptor.indextank.api.EmbeddedIndexEngine.java
@SuppressWarnings("static-access") private static Options getOptions() { Option baseDir = OptionBuilder.withArgName("base-dir").hasArg().isRequired() .withDescription("The basint e dir").withLongOpt("dir").create("d"); Option basePort = OptionBuilder.withArgName("base-port").hasArg().withDescription("The base port") .withLongOpt("port").create("p"); Option boostSize = OptionBuilder.withArgName("boosts-size").hasArg() .withDescription("Number of available boosts").withLongOpt("boosts").create("b"); Option rtiSize = OptionBuilder.withArgName("rti-size").hasArg() .withDescription("The size limit for the RTI").withLongOpt("rti-size").create("rs"); Option help = OptionBuilder.withDescription("displays this help").withLongOpt("help").create("h"); Option snippets = OptionBuilder.withDescription("Allow snippet generation and field fetching.") .withLongOpt("snippets").create("sn"); Option recover = OptionBuilder.withDescription("Recover documents from the storage.").withLongOpt("recover") .create("r"); Option indexCode = OptionBuilder.withArgName("code").hasArg().isRequired() .withDescription("the index code this indexengine has").withLongOpt("index-code").create("ic"); Option environment = OptionBuilder.withArgName("environment").hasArg().isRequired() .withDescription("environment prefix").withLongOpt("environment-prefix").create("env"); /*//from www . j a v a2s. co m * Analyzer argument should receive a JSON string with the following root structure: * - factory: a java type that implements the following static method: org.apache.lucene.analysis.Analyzer buildAnalyzer(Map). * - configuration: a JSON object to be passed to the buildAnalyzer method. */ Option analyzer = OptionBuilder.withArgName("analyzer").hasArg().withDescription("specific analyzer") .withLongOpt("analyzer").create("an"); Option configFile = OptionBuilder.withArgName("conf-file").hasArg().withDescription("configuration file") .withLongOpt("conf-file").create("cf"); Option loadState = OptionBuilder.withArgName("load") .withDescription( "if present, the index engine will try to restore its state" + "from the serialized form.") .withLongOpt("load-state").create("l"); Option suggest = OptionBuilder.withArgName("suggest").hasArg() .withDescription("if present, loads the suggest/autocomplete system.").withLongOpt("suggest") .create("su"); Option facets = OptionBuilder.withArgName("facets") .withDescription("if present, performs facetings queries.").withLongOpt("facets").create("fa"); Option functions = OptionBuilder.withArgName("functions").hasArg() .withDescription( "list of '|' separated scoring functions, each of which has the form <id>:<definition>.") .withLongOpt("functions").create("fn"); Option didyoumean = OptionBuilder.withLongOpt("didyoumean").withDescription( "if present, performs 'did you mean?' suggestions on queries. Requires --suggest documents.") .create("dym"); Option storage = OptionBuilder.withLongOpt("storage").hasArg() .withDescription( "if present, specifies a storage backend. Options are 'bdb' and 'ram'. Defaults to 'ram'.") .create("st"); Option bdbCache = OptionBuilder.withLongOpt("bdb-cache").hasArg().withDescription( "if present, specifies the size of the berkeleyDb cache per thread, in megabytes. Defaults to 100MB.") .create("bc"); Options options = new Options(); options.addOption(baseDir); options.addOption(basePort); options.addOption(boostSize); options.addOption(help); options.addOption(snippets); options.addOption(recover); options.addOption(indexCode); options.addOption(rtiSize); options.addOption(loadState); options.addOption(suggest); options.addOption(facets); options.addOption(functions); options.addOption(environment); options.addOption(analyzer); options.addOption(didyoumean); options.addOption(configFile); options.addOption(storage); options.addOption(bdbCache); return options; }
From source file:com.jagornet.dhcp.server.JagornetDhcpServer.java
/** * Setup command line options.//from ww w . j av a 2 s . c o m */ @SuppressWarnings("static-access") private void setupOptions() { Option configFileOption = OptionBuilder.withLongOpt("configfile").withArgName("filename") .withDescription("Configuration file (default = " + DEFAULT_CONFIG_FILENAME + ").").hasArg() .create("c"); options.addOption(configFileOption); Option portOption = OptionBuilder.withLongOpt("v6port").withArgName("portnum") .withDescription("DHCPv6 Port number (default = 547).").hasArg().create("6p"); options.addOption(portOption); Option mcastOption = OptionBuilder.withLongOpt("v6mcast").withArgName("interfaces") .withDescription("DHCPv6 Multicast support (default = none). " + "Use this option without arguments to instruct the server to bind to all " + "multicast-enabled IPv6 interfaces on the host. Optionally, use arguments " + "to list specific interfaces, separated by spaces.") .hasOptionalArgs().create("6m"); options.addOption(mcastOption); Option ucastOption = OptionBuilder.withLongOpt("v6ucast").withArgName("addresses") .withDescription("DHCPv6 Unicast addresses (default = all IPv6 addresses). " + "Use this option to instruct the server to bind to a specific list " + "of global IPv6 addresses, separated by spaces. These addresses " + "should be configured on one or more DHCPv6 relay agents connected " + "to DHCPv6 client links.") .hasOptionalArgs().create("6u"); options.addOption(ucastOption); Option v4BcastOption = OptionBuilder.withLongOpt("v4bcast").withArgName("interface") .withDescription("DHCPv4 broadcast support (default = none). " + "Use this option to specify the interface for the server to " + "receive and send broadcast DHCPv4 packets. Only one interface " + "may be specified. All other interfaces on the host will only " + "receive and send unicast traffic. The default IPv4 address on " + "the specified interface will be used for determining the " + "DHCPv4 client link within the server configuration file.") .hasArg().create("4b"); options.addOption(v4BcastOption); Option v4UcastOption = OptionBuilder.withLongOpt("v4ucast").withArgName("addresses") .withDescription("DHCPv4 Unicast addresses (default = all IPv4 addresses). " + "Use this option to instruct the server to bind to a specific list " + "of IPv4 addresses, separated by spaces. These addresses " + "should be configured on one or more DHCPv4 relay agents connected " + "to DHCPv4 client links.") .hasOptionalArgs().create("4u"); options.addOption(v4UcastOption); Option v4PortOption = OptionBuilder.withLongOpt("v4port").withArgName("portnum") .withDescription("DHCPv4 Port number (default = 67).").hasArg().create("4p"); options.addOption(v4PortOption); Option testConfigFileOption = OptionBuilder.withLongOpt("test-configfile").withArgName("filename") .withDescription("Test configuration file, then exit.").hasArg().create("tc"); options.addOption(testConfigFileOption); Option listIfOption = new Option("li", "list-interfaces", false, "Show detailed host interface list, then exit."); options.addOption(listIfOption); Option versionOption = new Option("v", "version", false, "Show version information, then exit."); options.addOption(versionOption); Option helpOption = new Option("?", "help", false, "Show this help page."); options.addOption(helpOption); }
From source file:com.aliyun.odps.ship.common.OptionsBuilder.java
public static Options getGlobalOptions() { Options opts = new Options(); opts.addOption(OptionBuilder.withLongOpt(Constants.CHARSET) .withDescription("specify file charset, default " + Constants.IGNORE_CHARSET + ". set " + Constants.IGNORE_CHARSET + " to download raw data") .hasArg().withArgName("ARG").create("c")); opts.addOption(OptionBuilder.withLongOpt(Constants.FIELD_DELIMITER) .withDescription("specify field delimiter, default " + Util.toHumanReadableString(Constants.DEFAULT_FIELD_DELIMITER)) .hasArg().withArgName("ARG").create("fd")); opts.addOption(OptionBuilder.withLongOpt(Constants.RECORD_DELIMITER) .withDescription("specify record delimiter, default " + Util.toHumanReadableString(Constants.DEFAULT_RECORD_DELIMITER)) .hasArg().withArgName("ARG").create("rd")); opts.addOption(OptionBuilder.withLongOpt(Constants.DATE_FORMAT_PATTERN) .withDescription("specify date format pattern, default " + Constants.DEFAULT_DATE_FORMAT_PATTERN) .hasArg().withArgName("ARG").create("dfp")); opts.addOption(OptionBuilder.withLongOpt(Constants.NULL_INDICATOR) .withDescription("specify null indicator string, default " + Util.toHumanReadableString(Constants.DEFAULT_NULL_INDICATOR)) .hasArg().withArgName("ARG").create("ni")); opts.addOption(OptionBuilder.withLongOpt(Constants.TIME_ZONE) .withDescription(/*from w w w . jav a 2s.c o m*/ "time zone, default local timezone: " + Calendar.getInstance().getTimeZone().getID()) .hasArg().withArgName("ARG").create("tz")); opts.addOption(OptionBuilder.withLongOpt(Constants.COMPRESS).withDescription("compress, default true") .hasArg().withArgName("ARG").create("cp")); opts.addOption(OptionBuilder.withLongOpt(Constants.HEADER) .withDescription("if local file should have table header, default " + Constants.DEFAULT_HEADER) .hasArg().withArgName("ARG").create("h")); opts.addOption(OptionBuilder.withLongOpt(Constants.SESSION_DIR) .withDescription("set session dir, default " + Constants.DEFAULT_SESSION_DIR).hasArg() .withArgName("ARG").create("sd")); opts.addOption(OptionBuilder.withLongOpt(Constants.THREADS) .withDescription("number of threads, default " + Constants.DEFAULT_THREADS).hasArg() .withArgName("ARG").create()); return opts; }
From source file:com.facebook.presto.accumulo.tools.PaginationTask.java
@SuppressWarnings("static-access") @Override/*from ww w.j a v a2 s . c om*/ public Options getOptions() { Options opts = new Options(); opts.addOption(OptionBuilder.withLongOpt("host").withDescription("Presto server host name").hasArg() .isRequired().create(HOST_OPT)); opts.addOption(OptionBuilder.withLongOpt("port").withDescription("Presto server port").hasArg().isRequired() .create(PORT_OPT)); opts.addOption(OptionBuilder.withLongOpt("file").withDescription("File containing SQL query to execute") .hasArg().isRequired().create(QUERY_FILE_OPT)); opts.addOption(OptionBuilder.withLongOpt("columns") .withDescription("Columns returned from the SQL SELECT, in order").hasArgs().isRequired() .create(COLUMNS_OPT)); opts.addOption(OptionBuilder.withLongOpt("size").withDescription("Page size. Default 20 rows per page") .hasArg().create(PAGE_SIZE_OPT)); return opts; }
From source file:net.palette_software.pet.restart.CliControl.java
static void createCommandLineOptions(Options options) { options.addOption("h", "help", false, "This help."); options.addOption("v", "version", false, "Print version information."); options.addOption("a", "restart", false, "Restart all processes one-by-one."); options.addOption("rv", "restart-vizql", false, "Restart VizQL workers."); options.addOption("rc", "restart-cache", false, "Restart Cache Server."); options.addOption("s", "simulation", false, "Simulate all the restarts."); options.addOption("i", "install", false, "Enable Balancer-manager."); options.addOption("rb", "restart-backgrounder", false, "Restart Backgrounder workers."); options.addOption("rp", "restart-vizportal", false, "Restart Vizportal workers."); options.addOption("rd", "restart-dataserver", false, "Restart Data Server workers."); options.addOption("pg", "reload-postgres", false, "Send reload signal to repository."); options.addOption("ra", "reload-apache", false, "Reload gateway rules."); options.addOption("f", "force", false, "Disable JMX, send signals immediately (non-graceful)."); options.addOption(OptionBuilder.withLongOpt("jmx-polling-time").withDescription("JMX data polling time") .hasArg().withArgName("SECONDS").create()); options.addOption(OptionBuilder.withLongOpt("wait").withDescription("Waiting time between jobs").hasArg() .withArgName("SECONDS").create()); options.addOption(OptionBuilder.withLongOpt("wait-errors") .withDescription("Waiting time after errors/retries").hasArg().withArgName("SECONDS").create()); options.addOption(OptionBuilder.withLongOpt("force-restart-timeout") .withDescription("Force restart timeout").hasArg().withArgName("SECONDS").create()); options.addOption(OptionBuilder.withLongOpt("tabsvc-config-dir").withDescription("Path to tabsvc configs") .hasArg().withArgName("PATH").create()); options.addOption(OptionBuilder.withLongOpt("tableau-installation-dir") .withDescription("Path to Tableau Server installation directory").hasArg().withArgName("PATH") .create());/*from www. j a v a2s. co m*/ }
From source file:be.ugent.intec.halvade.HalvadeOptions.java
protected void createOptions() { Option optIn = OptionBuilder.withArgName("input").hasArg().isRequired(true) .withDescription("Input directory on hdfs containing fastq files.").create("I"); Option optOut = OptionBuilder.withArgName("output").hasArg().isRequired(true) .withDescription("Output directory on hdfs.").create("O"); Option optBin = OptionBuilder.withArgName("bin.tar.gz").hasArg().isRequired(true) .withDescription("The tarred file containing all binary files located on HDFS.").create("B"); Option optRef = OptionBuilder.withArgName("reference").hasArg().isRequired(true).withDescription( "Name of the fasta file name of the reference (without extension) on HDFS. Make sure the BWA index has the same prefix.") .create("R"); Option optNodes = OptionBuilder.withArgName("nodes").hasArg().isRequired(true) .withDescription("Sets the number of nodes in this cluster.").withLongOpt("nodes").create("N"); Option optVcores = OptionBuilder.withArgName("cores").hasArg().isRequired(true) .withDescription("Sets the available cpu cores per node in this cluster.").withLongOpt("vcores") .create("C"); Option optMem = OptionBuilder.withArgName("gb").hasArg().isRequired(true) .withDescription("Sets the available memory [in GB] per node in this cluster.").withLongOpt("mem") .create("M"); Option optMmem = OptionBuilder.withArgName("gb").hasArg() .withDescription("Overrides the maximum map container memory [in GB].").withLongOpt("mapmem") .create();/*from w w w .j a va 2 s .c o m*/ Option optRmem = OptionBuilder.withArgName("gb").hasArg() .withDescription("Overrides the maximum reduce container memory [in GB].").withLongOpt("redmem") .create(); Option optSites = OptionBuilder.withArgName("snpDBa,snpDBb").hasArg().isRequired(true) .withDescription("Name of snpDB files for the genome on HDFS. If multiple separate with \',\'.") .create("D"); Option optStarGenome = OptionBuilder.withArgName("stargenome").hasArg() .withDescription("Directory on HDFS containing all STAR genome files").withLongOpt("star") .create("S"); Option optTmp = OptionBuilder.withArgName("dir").hasArg() .withDescription("Sets the location for temporary files on every node [/tmp/halvade/].") .withLongOpt("tmp").create(); Option optrefdir = OptionBuilder.withArgName("dir").hasArg().withDescription( "Sets the folder containing all the reference files for BWA or STAR and GATK on every node [tmp directory].") .withLongOpt("refdir").create(); Option optJava = OptionBuilder.withArgName("java").hasArg() .withDescription("Set location of java binary to use [must be 1.7+].").create("J"); // "ID:" + RGID + " LB:" + RGLB + " PL:" + RGPL + " PU:" + RGPU + " SM:" + RGSM Option optID = OptionBuilder.withArgName("RGID").hasArg() .withDescription("sets the RGID for the read-group.").withLongOpt("id").create(); Option optLB = OptionBuilder.withArgName("RGLB").hasArg() .withDescription("sets the RGLB for the read-group.").withLongOpt("lb").create(); Option optPL = OptionBuilder.withArgName("RGPL").hasArg() .withDescription("sets the RGPL for the read-group.").withLongOpt("pl").create(); Option optPU = OptionBuilder.withArgName("RGPU").hasArg() .withDescription("sets the RGPU for the read-group.").withLongOpt("pu").create(); Option optSM = OptionBuilder.withArgName("RGSM").hasArg() .withDescription("sets the RGSM for the read-group.").withLongOpt("sm").create(); Option optCov = OptionBuilder.withArgName("coverage").hasArg() .withDescription("Sets the coverage to better distribute the tasks.").withLongOpt("cov").create(); Option optScc = OptionBuilder.withArgName("scc").hasArg() .withDescription("Sets stand_call_conf for gatk Variant Caller.").withLongOpt("scc").create(); Option optSec = OptionBuilder.withArgName("sec").hasArg() .withDescription("Sets stand_emit_conf for gatk Variant Caller.").withLongOpt("sec").create(); Option optBed = OptionBuilder.withArgName("bedfile").hasArg() .withDescription("Sets the bed file containing relevant (Genes) regions which " + "will be used to split the genome into genomic regions.") .withLongOpt("bed").create(); Option optFilterBed = OptionBuilder.withArgName("bedfile").hasArg() .withDescription("Sets the bed file containing relevant (Exome) regions which " + " will be used to filter in the GATK steps.") .withLongOpt("fbed").create(); Option optGff = OptionBuilder.withArgName("gff").hasArg().withDescription( "Sets the gff file to be used with FeautreCounts. This is required to count reads per exon.") .withLongOpt("gff").create(); Option optstargtf = OptionBuilder.withArgName("gtf").hasArg() .withDescription("Sets the gtf file to be used within the STAR alignment.").withLongOpt("stargtf") .create(); Option optMpn = OptionBuilder.withArgName("tasks").hasArg() .withDescription("Overrides the number of map tasks running simultaneously on each node. ") .withLongOpt("mpn").create(); Option optRpn = OptionBuilder.withArgName("tasks").hasArg() .withDescription("Overrides the number of reduce tasks running simultaneously on each node. ") .withLongOpt("rpn").create(); Option optCustomArgs = OptionBuilder.withLongOpt("custom_args").withArgName("tool=args").hasArgs(2) .withValueSeparator() .withDescription( "Adds custom arguments for a tool. If a module in a tool is used, add the name after an underscore. " + "Possible values: " + getProgramNames()) .withLongOpt("CA").create(); Option optVerbose = OptionBuilder.withArgName("num").hasArg() .withDescription("Sets verbosity of debugging [2].").create("v"); Option optAln = OptionBuilder.withArgName("num").hasArg().withDescription( "Sets the aligner used in Halvade. Possible values are 0 (bwa aln+sampe)[default], 1 (bwa mem), 2 (bowtie2), 3 (cushaw2).") .withLongOpt("aln").create(); Option optReadsPerRegion = OptionBuilder.withArgName("file").hasArg().withDescription( "Give a file with read counts per region to better distribute the regions (split by readcount [default] or reorder regions by size [-reorder_regions]).") .withLongOpt("rpr").create(); //flags Option optSingle = OptionBuilder .withDescription("Sets the input files to single reads [default is paired-end reads].") .withLongOpt("single").create(); Option optCombine = OptionBuilder .withDescription("Just Combines the vcf on HDFS [out dir] and doesn't run the hadoop job.") .withLongOpt("combine").create(); Option optPp = OptionBuilder .withDescription( "Uses elPrep to preprocess the data for GATK, this requires more memory but is faster.") .withLongOpt("elprep").create(); Option optFilterDBsnp = OptionBuilder .withDescription("Use Bedtools to select the needed interval of dbsnp.").withLongOpt("filter_dbsnp") .create(); Option optJustAlign = OptionBuilder.withDescription("Only align the reads.").withLongOpt("justalign") .create("A"); Option optSmt = OptionBuilder.withDescription("Enable simultaneous multithreading.").withLongOpt("smt") .create(); Option optKeep = OptionBuilder.withDescription("Keep intermediate files.").withLongOpt("keep").create(); Option optHap = OptionBuilder .withDescription("Use HaplotypeCaller instead of UnifiedGenotyper for Variant Detection.") .withLongOpt("haplotypecaller").create("H"); Option optRna = OptionBuilder.withDescription( "Run the RNA Best Practices pipeline by Broad [default is DNA pipeline]. SG needs to be set for this.") .withLongOpt("rna").create(); Option optDry = OptionBuilder.withDescription( "Execute a dryrun, will calculate task size, split for regions etc, but not execute the MapReduce job.") .withLongOpt("dryrun").create(); Option optDrop = OptionBuilder .withDescription("Drop all paired-end reads where the pairs are aligned to different chromosomes.") .withLongOpt("drop").create(); Option optReportAll = OptionBuilder .withDescription("Reports all variants at the same location when combining variants.") .withLongOpt("report_all").create(); Option optBamIn = OptionBuilder .withDescription("Uses aligned bam as input files instead of unaligned fastq files.") .withLongOpt("bam").create(); Option optRedis = OptionBuilder.withDescription( "This will enable Halvade to redistribute resources when possible when not all containers are used.") .withLongOpt("redistribute").create(); Option optMergeBam = OptionBuilder.withDescription( "Merges all bam output from either bam input or the aligned reads from the fastq input files.") .withLongOpt("merge_bam").create(); Option optReorderRegions = OptionBuilder.withDescription( "Use the default split way but reorder tasks by size based on the read count file given by -rpr option.") .withLongOpt("reorder_regions").create(); Option optupdateRG = OptionBuilder .withDescription("Update the readgroup when reading from a BAM input file.") .withLongOpt("update_rg").create(); Option optCount = OptionBuilder .withDescription("Count the number of reads per reduce task (for debug purposes).") .withLongOpt("count").create(); Option optRemDup = OptionBuilder.withDescription("Remove PCR duplicates for GATK.") .withLongOpt("remove_dups").create(); Option optFixEnc = OptionBuilder .withDescription( "Fix the quality encoding of old (pre 1.8) Illumina fastq files to the new encoding.") .withLongOpt("illumina").create(); options.addOption(optIn); options.addOption(optOut); options.addOption(optRef); options.addOption(optSites); options.addOption(optBin); options.addOption(optTmp); options.addOption(optrefdir); options.addOption(optSingle); options.addOption(optAln); options.addOption(optID); options.addOption(optLB); options.addOption(optPL); options.addOption(optPU); options.addOption(optSM); options.addOption(optPp); options.addOption(optFilterDBsnp); options.addOption(optHap); options.addOption(optScc); options.addOption(optSec); options.addOption(optBed); options.addOption(optFilterBed); options.addOption(optJava); options.addOption(optCombine); options.addOption(optNodes); options.addOption(optVcores); options.addOption(optMem); options.addOption(optKeep); options.addOption(optJustAlign); // options.addOption(optCov); options.addOption(optMpn); options.addOption(optGff); options.addOption(optRpn); options.addOption(optDry); options.addOption(optDrop); options.addOption(optReportAll); options.addOption(optSmt); options.addOption(optRna); // options.addOption(optReadsPerRegion); options.addOption(optStarGenome); options.addOption(optBamIn); options.addOption(optCustomArgs); options.addOption(optRedis); options.addOption(optRmem); options.addOption(optMmem); options.addOption(optMergeBam); options.addOption(optVerbose); // options.addOption(optReorderRegions); options.addOption(optupdateRG); options.addOption(optCount); options.addOption(optRemDup); options.addOption(optstargtf); options.addOption(optFixEnc); }
From source file:com.upload.DcmSnd.java
private static CommandLine parse(String[] args) { Options opts = new Options(); OptionBuilder.withArgName("name"); OptionBuilder.hasArg();/*from w ww . j a v a 2 s .c o m*/ OptionBuilder.withDescription("set device name, use DCMSND by default"); opts.addOption(OptionBuilder.create("device")); OptionBuilder.withArgName("aet[@host][:port]"); OptionBuilder.hasArg(); OptionBuilder.withDescription("set AET, local address and listening port of local " + "Application Entity, use device name and pick up any valid " + "local address to bind the socket by default"); opts.addOption(OptionBuilder.create("L")); opts.addOption("ts1", false, "offer Default Transfer Syntax in " + "separate Presentation Context. By default offered with " + "Explicit VR Little Endian TS in one PC."); opts.addOption("fileref", false, "send objects without pixel data, but with a reference to " + "the DICOM file using DCM4CHE URI Referenced Transfer Syntax " + "to import DICOM objects on a given file system to a DCM4CHEE " + "archive."); OptionBuilder.withArgName("username"); OptionBuilder.hasArg(); OptionBuilder.withDescription( "enable User Identity Negotiation with specified username and " + " optional passcode"); opts.addOption(OptionBuilder.create("username")); OptionBuilder.withArgName("passcode"); OptionBuilder.hasArg(); OptionBuilder.withDescription( "optional passcode for User Identity Negotiation, " + "only effective with option -username"); opts.addOption(OptionBuilder.create("passcode")); opts.addOption("uidnegrsp", false, "request positive User Identity Negotation response, " + "only effective with option -username"); OptionBuilder.withArgName("NULL|3DES|AES"); OptionBuilder.hasArg(); OptionBuilder.withDescription("enable TLS connection without, 3DES or AES encryption"); opts.addOption(OptionBuilder.create("tls")); OptionGroup tlsProtocol = new OptionGroup(); tlsProtocol.addOption(new Option("tls1", "disable the use of SSLv3 and SSLv2 for TLS connections")); tlsProtocol.addOption(new Option("ssl3", "disable the use of TLSv1 and SSLv2 for TLS connections")); tlsProtocol.addOption(new Option("no_tls1", "disable the use of TLSv1 for TLS connections")); tlsProtocol.addOption(new Option("no_ssl3", "disable the use of SSLv3 for TLS connections")); tlsProtocol.addOption(new Option("no_ssl2", "disable the use of SSLv2 for TLS connections")); opts.addOptionGroup(tlsProtocol); opts.addOption("noclientauth", false, "disable client authentification for TLS"); OptionBuilder.withArgName("file|url"); OptionBuilder.hasArg(); OptionBuilder .withDescription("file path or URL of P12 or JKS keystore, resource:tls/test_sys_2.p12 by default"); opts.addOption(OptionBuilder.create("keystore")); OptionBuilder.withArgName("password"); OptionBuilder.hasArg(); OptionBuilder.withDescription("password for keystore file, 'secret' by default"); opts.addOption(OptionBuilder.create("keystorepw")); OptionBuilder.withArgName("password"); OptionBuilder.hasArg(); OptionBuilder .withDescription("password for accessing the key in the keystore, keystore password by default"); opts.addOption(OptionBuilder.create("keypw")); OptionBuilder.withArgName("file|url"); OptionBuilder.hasArg(); OptionBuilder.withDescription("file path or URL of JKS truststore, resource:tls/mesa_certs.jks by default"); opts.addOption(OptionBuilder.create("truststore")); OptionBuilder.withArgName("password"); OptionBuilder.hasArg(); OptionBuilder.withDescription("password for truststore file, 'secret' by default"); opts.addOption(OptionBuilder.create("truststorepw")); OptionBuilder.withArgName("aet@host:port"); OptionBuilder.hasArg(); OptionBuilder.withDescription("request storage commitment of (successfully) sent objects " + "afterwards in new association to specified remote " + "Application Entity"); opts.addOption(OptionBuilder.create("stgcmtae")); opts.addOption("stgcmt", false, "request storage commitment of (successfully) sent objects " + "afterwards in same association"); OptionBuilder.withArgName("attr=value"); OptionBuilder.hasArgs(); OptionBuilder.withValueSeparator('='); OptionBuilder.withDescription("Replace value of specified attribute " + "with specified value in transmitted objects. attr can be " + "specified by name or tag value (in hex), e.g. PatientName " + "or 00100010."); opts.addOption(OptionBuilder.create("set")); OptionBuilder.withArgName("salt"); OptionBuilder.hasArgs(); OptionBuilder.withDescription( "Anonymize the files. Set to 0 for a random anonymization (not repeatable) or 1 for a daily anonymization or another" + " value for a specific salt for reproducible anonymization (useful for allowing studies to be sent at a later date and still correctly named/associated)"); OptionBuilder.withLongOpt("anonymize"); opts.addOption(OptionBuilder.create("a")); OptionBuilder.withArgName("sx1[:sx2[:sx3]"); OptionBuilder.hasArgs(); OptionBuilder.withValueSeparator(':'); OptionBuilder.withDescription( "Suffix SOP [,Series [,Study]] " + "Instance UID with specified value[s] in transmitted objects."); opts.addOption(OptionBuilder.create("setuid")); OptionBuilder.withArgName("maxops"); OptionBuilder.hasArg(); OptionBuilder.withDescription("maximum number of outstanding operations it may invoke " + "asynchronously, unlimited by default."); opts.addOption(OptionBuilder.create("async")); opts.addOption("pdv1", false, "send only one PDV in one P-Data-TF PDU, " + "pack command and data PDV in one P-DATA-TF PDU by default."); opts.addOption("tcpdelay", false, "set TCP_NODELAY socket option to false, true by default"); OptionBuilder.withArgName("ms"); OptionBuilder.hasArg(); OptionBuilder.withDescription("timeout in ms for TCP connect, no timeout by default"); opts.addOption(OptionBuilder.create("connectTO")); OptionBuilder.withArgName("ms"); OptionBuilder.hasArg(); OptionBuilder.withDescription("delay in ms for Socket close after sending A-ABORT, " + "50ms by default"); opts.addOption(OptionBuilder.create("soclosedelay")); OptionBuilder.withArgName("ms"); OptionBuilder.hasArg(); OptionBuilder.withDescription("delay in ms for closing the listening socket, " + "1000ms by default"); opts.addOption(OptionBuilder.create("shutdowndelay")); OptionBuilder.withArgName("ms"); OptionBuilder.hasArg(); OptionBuilder.withDescription("period in ms to check for outstanding DIMSE-RSP, " + "10s by default"); opts.addOption(OptionBuilder.create("reaper")); OptionBuilder.withArgName("ms"); OptionBuilder.hasArg(); OptionBuilder.withDescription("timeout in ms for receiving DIMSE-RSP, 10s by default"); opts.addOption(OptionBuilder.create("rspTO")); OptionBuilder.withArgName("ms"); OptionBuilder.hasArg(); OptionBuilder.withDescription("timeout in ms for receiving A-ASSOCIATE-AC, 5s by default"); opts.addOption(OptionBuilder.create("acceptTO")); OptionBuilder.withArgName("ms"); OptionBuilder.hasArg(); OptionBuilder.withDescription("timeout in ms for receiving A-RELEASE-RP, 5s by default"); opts.addOption(OptionBuilder.create("releaseTO")); OptionBuilder.withArgName("KB"); OptionBuilder.hasArg(); OptionBuilder.withDescription("maximal length in KB of received P-DATA-TF PDUs, 16KB by default"); opts.addOption(OptionBuilder.create("rcvpdulen")); OptionBuilder.withArgName("KB"); OptionBuilder.hasArg(); OptionBuilder.withDescription("maximal length in KB of sent P-DATA-TF PDUs, 16KB by default"); opts.addOption(OptionBuilder.create("sndpdulen")); OptionBuilder.withArgName("KB"); OptionBuilder.hasArg(); OptionBuilder.withDescription("set SO_RCVBUF socket option to specified value in KB"); opts.addOption(OptionBuilder.create("sorcvbuf")); OptionBuilder.withArgName("KB"); OptionBuilder.hasArg(); OptionBuilder.withDescription("set SO_SNDBUF socket option to specified value in KB"); opts.addOption(OptionBuilder.create("sosndbuf")); OptionBuilder.withArgName("KB"); OptionBuilder.hasArg(); OptionBuilder.withDescription("transcoder buffer size in KB, 1KB by default"); opts.addOption(OptionBuilder.create("bufsize")); OptionBuilder.withArgName("count"); OptionBuilder.hasArg(); OptionBuilder.withDescription("Batch size - Number of files to be sent in each batch, " + "where a storage commit is done between batches "); opts.addOption(OptionBuilder.create("batchsize")); opts.addOption("lowprior", false, "LOW priority of the C-STORE operation, MEDIUM by default"); opts.addOption("highprior", false, "HIGH priority of the C-STORE operation, MEDIUM by default"); opts.addOption("h", "help", false, "print this message"); opts.addOption("V", "version", false, "print the version information and exit"); CommandLine cl = null; try { cl = new GnuParser().parse(opts, args); } catch (ParseException e) { exit("dcmsnd: " + e.getMessage()); throw new RuntimeException("unreachable"); } if (cl.hasOption('V')) { Package p = DcmSnd.class.getPackage(); System.out.println("dcmsnd v" + p.getImplementationVersion()); // System.exit(0); } if (cl.hasOption('h') || cl.getArgList().size() < 2) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(USAGE, DESCRIPTION, opts, EXAMPLE); // System.exit(0); } return cl; }