All Classes
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All Classes Interface Summary Class Summary Enum Summary Exception Summary Error Summary Annotation Types Summary Class Description AbstractAction This class define an abstract ActionAbstractBAM2SAMModule This class define a module for converting BAM files into SAM.AbstractClusterTaskScheduler This class is a scheduler for task running on a cluster.AbstractConcatInputStream This class define an InputStream that concatenate InputStream.AbstractEoulsanRuntime This class define an abstract EoulsanRuntime.AbstractEoulsanRuntime.EoulsanExecMode This Enum define the Eoulsan execution mode.AbstractExecutorInterpreter This class define an abstract executor interpreter that contains the default implementation of theexecute()
method that use aProcessBuilder
.AbstractExpressionModule This abstract class define and parse arguments for the expression module.AbstractFilterAndMapReadsModule This class define an abstract module for read filtering, mapping and alignments filtering.AbstractInfoAction This class define an abstract action that show the some Eoulsan configuration and available modulesAbstractMetadata This abstract class defines methods for metadata.AbstractModule This class define an abstract Module.AbstractParameterToolElement This class define an abstract class for tool element parameters.AbstractPort Abstract class that define a port.AbstractPorts<E extends Port> This class define a basic implementation of a Ports class.AbstractReadsFilterModule This class define an abstract module for read filtering.AbstractReadsMapperModule This class define an abstract module for read mapping.AbstractRequirement This class define an abstract requirement.AbstractResourceLoader<S> This class define an abstract resource loader.AbstractRExecutor This class define an abstract RExecutor.AbstractSAM2BAMModule This class define a module for converting SAM files into BAM.AbstractSAM2FASTQModule This class define a module for converting SAM files into BAM.AbstractSAMFilterModule This class define an abstract module for alignments filtering.AbstractSplice2BEDModule This class define a module for converting SAM files into BED.AbstractStep This class define a step of the workflow.AbstractTaskScheduler This class define an abstract task scheduler.AbstractToolElement This class define an abstract tool element.AbstractWorkflow This class define a Workflow.Action This interface define an action.ActionService This class define a service to retrieve an ActionAdditionalAnnotationDataProtocol This class define a additional annotation protocol.AnnotationDataProtocol This class define a annotation protocol.ApacheCommonCompressionCodecs This class allow to create input and output stream for compression codecs of the Apache Common Compression library.BAM2SAMLocalModule This class define a module for converting BAM files into SAM.BAMMerger This class define a merger class for SAM files.BAMSplitter This class define a splitter class for BAM files.BasicUI This class define a basic UI for Eoulsan.BedToolsModule This class uses tools from the BEDTools suite.BooleanParameterToolElement This class define a boolean tool element parameter.BpipeTaskScheduler This class allow to submit, stop and get the status of jobs using Bpipe scheduler wrappers.BufferedHandler This class define a buffered handler.BundledScriptBpipeTaskScheduler This class define an abstract scheduler that use a bpipe script bundled in Eoulsan distribution.ByteCountInputStream This filter class allow to count the number of bytes read by an inputStream.ByteCountOutputStream This class define a filter that count the number of written bytes by an InputStream.Checker This interface define a checker.CheckerModule This class is a module that launch checkers.CheckStore This class define a storage where some results of the checker can be save for later reuse by other checkers.CheetahInterpreter This class create a Cheetah interpreter, it can build a command line tool from command tag from Galaxy tool XML file.ChIPSeqDataFormats This class contains the definition of some DataFormats for ChiP-Seq.ClassLoaderObjectInputStream This class allow to use ObjectInputStream with a ClassLoader that is not the default bootstrap ClassLoader.ClassPathResourceLoader<S> This class allow to define a resource loader for resources in the class path.CLIMergingAnySAMOutputFormat<K> ClusterCombinedTaskScheduler This class defined a combined task scheduler for cluster mode.ClusterExecAction This class define the cluster exec Action.ClusterJobEmergencyStopTask This class define an EmergencyStopTask for cluster Jobs.ClusterTaskAction This class define a action to launch a task on a cluster.ClusterTaskScheduler This interface define a cluster task scheduler.ClusterTaskScheduler.StatusResult This class define a Status result return by the statusJob() method of the interface.ClusterTaskScheduler.StatusValue This enum define the values of the status of a job.ClusterTaskSchedulerService This class define a service to retrieve a ClusterTaskScheduler.CollectionUtils This class define an utility class that contains useful methods for collections.CombinedTaskScheduler This class defined a combined task scheduler that use several context schedulers according to the parallelization mode of the step.CommandStep This class define a step based on a Command object (workflow file).CommandWorkflow This class define a workflow based on a Command object (workflow file).CommandWorkflowModel This class define the workflow model object of Eoulsan.CommandWorkflowParser This class allow parse the workflow file.CommandWorkflowParser.StepOutputPort Common This class define common constants.CommonHadoop This class define common constants and other methods specific to Hadoop mode.CompressedSplitFastqLineReader ConditionalToolElement This class define a conditional tool element.ContextUtil Utility methods to allow applications to deal with inconsistencies between MapReduce Context Objects API between hadoop-0.20 and later versions.ContextUtils This class define utility methods on Context.CopyDesignAndWorkflowFilesToOutputModule This module copy design and workflow file to output directory.CopyInputDataModule Copy input files of a format in another location or in different compression format.CopyOutputDataModule Copy output files of a step with a specified format to the output directory.Counters This class define the counters names used in this package.CounterSequenceFile This interface extends SequenceFile to add a getCount() method that allow to get the count of the read entries.CountSplicedReadsModule This step computes how many spliced alignments there are in a SAM file.CreateDesignAction This class define an action to create design file.CreateHadoopJarAction This class define an action to create hadoop jar file.Data This interface define data used by ports.DataFile This class define a DataFile.DataFileDataPath This class define a bridge between Kenetre DataPath objects and Eoulsan DataFile objects.DataFileDistCp This class allow to copy and transform data in a distributed manner.DataFileDistCp.DistCpMapper This inner class define the mapper class for DataSourceDistCp map-reduce job.DataFileGenomeDescStorage This class define a storage for genome description files using DataFile API.DataFileGenomeIndexStorage This class define a storage for genome indexes using DataFile API.DataFileGenomeMapperIndexer This class define a genome mapper indexer.DataFileMetadata This class define source metadataDataFiles This class contains utility methods on DataFile objects.DataFileStorage This class define a storage using DataFile API.DataFormat This interface define a DataFormat.DataFormatConverter This class allow to copy and transform data while copying.DataFormatRegistry this class register DataFormat to allow get the DataFormat of a file from its filename.DataFormats This class contains the definition of some DataFormats.DataList This class define a data list.DataMetadata This interface define metadata of data objects.DataMetadataStorage This class define a storage for data metadata of all files generated by the workflow.DataProtocol This interface define a protocol.DataProtocolService This class define a service to retrieve a DataProtocol.DataToolElement The Class ToolOutputsData.DataUtils This class define an utility on data object.DeepToolsModule This class uses tools from the DeepTools suite.DefaultDesignReader This class allow to read a design file whatever the underlying design format.DefaultExecutorInterpreter This class define the default executor interpreter.DefineDataFormatToDownload This Step allow to define the list of the formats of the files to download at the end of a Hadoop execution.DeprecatedDataProtocol This class define a deprecated protocol.DESeq2 This class contains methods to run the differential analysis module DESeq2.DESeq2.FitType Enum for the fitType option in DESeq2 related to the dispersion estimation.DESeq2.SizeFactorsType Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.DESeq2.StatisticTest Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysisDESeq2DesignChecker This class define a Checker on the design for DESeq2 analyzes.DESeq2Module Class to run the differential analysis with DEseq2Design This interface defines the design.DesignBuilder This class allow to easily build Design object from files paths.DesignFactory This class is a factory for experimental design.DesignFormatFinderInputStream This class allow to automatically detect the format of a design file.DesignMetadata This interface defines the design metadata.DesignMetadataImpl This class defines the default implementation of the design metadata.DesignModule This class define a design module.DesignReader This interface define a DesignReader.DesignUtils Utils methods for Design.DesignWriter This interface define a writer for designs.DiffAna This class create and launch a R script to compute differential analysis.DiffAna.DispersionFitType Dispersion estimation fitType enum for DESeq differential analysisDiffAna.DispersionMethod Dispersion estimation method enum for DESeq differential analysisDiffAna.DispersionSharingMode Dispersion estimation sharingMode enum for DESeq differential analysisDiffAnaModule This class define the module of differential analysis in local mode.DiffanaResultsAnnotationModule This class define a module that create annotated expression files in TSV, ODS or XLSX format.DistCp A Map-reduce program to recursively copy directories between different file-systems.DistCp.DuplicationException An exception class for duplicated source files.DistributedLock Distributed locking via ZooKeeper.DistributedLocker This class implements a locker using Zookeeper based on Twiter's DistributedLock class.DockerExecutorInterpreter This class define a Docker executor interpreter.DockerRequirement This class define a Docker requirement.DockerRExecutor This class define a Docker RExecutor.DummyGeneratorModule This class implements a dummy generator module that create an empty file.DummyTaskScheduler This class define a Dummy cluster scheduler.EmergencyStopTask This interface define a task that will executed if the execution of the workflow fail.EmergencyStopTasks This class define a class where the emergency tasks are storedEmptyFileQC Empty file FastQC module.EmptyToolElement This class define an empty tool element.Eoulsan1DesignReader This class define a design reader for limma design files.Eoulsan1DesignWriter This class implements a writer for limma design files.Eoulsan2DesignReader This class define a design reader for Eoulsan 2 design file.Eoulsan2DesignWriter This class implements a writer for Eoulsan 2 design files.EoulsanAnnotationUtils This class contains annotation utilities.EoulsanDockerManager This class define a Docker manager configurated with Eoulsan settings.EoulsanError A nestable Eoulsan error.EoulsanException A nestable Eoulsan exception.EoulsanITRuntimeException This class define a runtime exception for integration tests.EoulsanLogger This class allow to change the logger name for all Eoulsan classes.EoulsanRuntime This class store the only Eoulsan runtime instance.EoulsanRuntimeException A nestable Eoulsan exception.EoulsanTranslatorUtils This class define Kenetre translator utility glue methods for Eoulsan.ExecAction This class define the Local exec Action.ExecFileLock This class define a lock file.ExecJarHadoopAction This class define an action that allow to execute a jar on an Hadoop cluster.ExecLock This class define a lock to prevent execution of a process simultaneously on multiples JVM.ExecutionMode This class define an enum for the execution mode of Eoulsan.Executor This class is the executor for running all the steps of an analysis.ExecutorArguments This class contains arguments for the Executor.ExecutorInterpreter This interface define a executor interpreter for Galaxy tools.Experiment This interface defines an experiment.ExperimentImpl This class defines the default implementation of an experiment.ExperimentMetadata This interface defines the experiment metadata.ExperimentSample This interface defines the experiment sample.ExperimentSampleImpl This class defines the default implementation of the experiment sample.ExperimentSampleMetadata This inteface defines the experiment sample metadata.ExperimentSampleMetadataImpl This class defines the default implementation of the experiment sample metadata.ExpressionCounterCounter This enum define counters for the expression step.ExpressionCounterUtils This class define some glue methods between Eoulsan and Kenetre.ExpressionHadoopModule This class is the main class for the expression program of the reads in hadoop mode.ExpressionInputPreprocessor This class define a preprocessor for expression reports.ExpressionLocalModule This class is the module to compute expression in local modeExpressionMapper Mapper for the expression estimation.ExpressionMerger This class define a merger class for expression files.ExpressionOutputFormat This class define a expression output format.ExpressionRecordWriter This class define a RecordWriter for expression files.ExpressionReducer Reducer for the expression estimation.ExpressionResultsAnnotationModule This class define a module that create annotated expression files in TSV, ODS or XLSX format.ExpressionSAMOutputMapper Mapper for the expression estimation with a SAM output.ExpressionSplitter This class define a splitter class for expression files.ExpressionToMatrixModule This class define a class that allow to merge expression file into a matrix file.FailModule This module is a module that always fails.FakeModule This module is a fake module.FastQCInputPreprocessor This class define a preprocessor for FastQC reports.FastQCModule This class define a module that compute QC report using FastQC.FastQCRuntimePatcher This class to patch FastQC to be compatible with Hadoop.FastqInputFormat This class define an InputFormat for FASTQ files for the Hadoop MapReduce framework.FastqLineRecordReader Treats keys as offset in file and value as line.FastqMerger This class define a merger class for FASTQ files.FastqOutputFormat This class define a FASTQ output format.FastqRecordReader This class define a RecordReader for FASTQ files for the Hadoop MapReduce framework.FastqRecordWriter This class define a RecordWriter for FASTQ files.FastqSequenceFile This class define a SequenceFile for FASTQ files.FastqSplitter This class define a splitter class for FASTQ files.FeatureCountsInputPreprocessor This class define a preprocessor for FeatureCounts reports.FileCharsets This class define default charsets.FileConcatInputStream This class define an InputStream that concatenate files in an InputStream.FileDataProtocol This class implements a File Protocol.FileNaming This class contains methods to create workflow data file names.FileNamingParsingRuntimeException This class define a runtime exception for filename parsing errors.FileResourceLoader<S> This class allow to define a resource loader for files.FilterAndMapReadsHadoopModule This class define a Step that filter and map read in Hadoop mode.FinalExpressionFeaturesCreator This class generates the final expression file after counting the alignments for each feature with HTSeq-count.FirstModule This class define a first module that do nothing.FloatParameterToolElement This class define a float tool element parameter.FormatsAction This class define an action that show the list of available formats.FTPPathDataProtocol This class define the FTP protocol in Hadoop mode.FTPURLDataProtocol This class define the ftp protocol in local mode.GalaxyToolInterpreter This class create an interpreter to tool xml file from Galaxy.GalaxyToolModule The Class GalaxyToolStep.GalaxyToolXMLParserUtils This class define static utils methods to extract data in Galaxy tool XML file.Generator This annotation is used to mark a step class that is a generator with user custom parameters.GenericExecutorInterpreter This class define a generic executor interpreter.GenericStorageGeneratorModule This module allow to easily store output of generator to avoid computation at each Eoulsan startup.GenomeChecker This class define a Checker on genome FASTA files.GenomeDataProtocol This class define a genome protocol.GenomeDescriptionCreator This class define a genome description creator.GenomeDescriptionGeneratorModule This class implements a genome description generator module.GenomeMapperIndexGeneratorModule This class define a module that generate a genome mapper index.GFFChecker This class define a Checker on GFF annotation.GFFDataProtocol This class define a annotation protocol.GFFFastaGeneratorModule This generator allow to generate a genome fasta file from the fasta section of a GFF file.Globals This class contains globals constants for the application.GTFChecker This class define a Checker on GTF annotation.GTFDataProtocol This class define a annotation protocol.HadoopBamUtils HadoopCompatible This annotation is used to mark a plug-in class as usable in hadoop mode and local mode.HadoopCompatibleTaskScheduler This class is a scheduler for tasks from step with the @HadoopComptible annotation in Hadoop mode.HadoopCompatibleTaskScheduler.HadoopCompatibleMapper HadoopCompressionCodecs This class allow to create input and output stream for compression codec of Hadoop.HadoopEoulsanRuntime This class define the Runtime to execute low level IO operation for Eoulsan in Hadoop mode.HadoopExecAction This class launch Eoulsan in hadoop mode.HadoopInfo This class show in log some Hadoop information.HadoopJarRepackager This class allow to repackage the application.HadoopJobEmergencyStopTask This class define an EmergencyStopTask for Hadoop Jobs.HadoopMappingUtils This class contains utility methods for the Hadoop mapping package classes.HadoopOnly This annotation is used to mark a plug-in class as usable in hadoop mode only.HadoopReporter This class define a Hadoop reporter.HadoopReporterIncrementer This class define a Hadoop reporter.HadoopUploadModule This class define a module for Hadoop file uploading.HDFSDataDownloadModule This class define a download module that retrieve data from HDFS at the end of an analysis.HDFSPathDataProtocol This class define the HDFS protocol in Hadoop mode.HTCondorTaskScheduler This class define a HTCondor cluster scheduler using a Bpipe script.HTMLReportArchiveNeigborClass Empty class for patching the HTMLReportArchive class of FastQC.HTTPPathDataProtocol This class define the HTTP protocol in Hadoop mode.HTTPSPathDataProtocol This class define the HTTP protocol in Hadoop mode.HTTPSURLDataProtocol This class define the http protocol in local mode.HTTPURLDataProtocol This class define the http protocol in local mode.IDRModule This class defines the IDR quality check step.ImportModule This class define a import step.InfoAction This class define an action that show the Eoulsan configurationInfos This class gathers information about Eoulsan configuration and system environment.Infos.Info This class define an info.InputPort This interface define an input port of a step.InputPorts This interface define a group of input ports.InputPortsBuilder This class allow to easily create input ports for a step.InputPreprocessor This interface define a preprocessor for MultiQC input data.InputPreprocessorService This class define a service to retrieve a InputPreprocessor.IntegerParameterToolElement This class define an integer tool element parameter.IntegrationTestAction This class launch integration test with Testng class.JarRepack This class allow to repackage a jar file.LanternaUI This class define an UI using Lanterna library.LinuxCpuInfo Get information about processor on Linux systems.LinuxInfo This class define a linux info file parser.LinuxMemInfo Get information about memory on Linux systemsLocalEoulsanRuntime This class define the Runtime to execute low level IO operation for Eoulsan in local mode.LocalOnly This annotation is used to mark a plug-in class as usable in local mode only.LocalUploadModule This class define a Step for local mode file uploading.Locker This interface define an interface for the global execution locker.LockerUtils Utility class for the locker classes.MACS2Module This class defines the macs2 peak-calling step.Main This class is the main class.MainCLI Main class in local mode.MainHadoop Main class in Hadoop mode.MapperIndexDataFormat This class define a DataFormat from an XML file.MapperInputPreprocessor This class define a preprocessor for mapper reports.MappingCounters This enum define the names of the counters of the steps of this package.MapReduceUtils This class contains utility method to easily manipulate the new Hadoop MapReduce API.MatrixToCellRangerMatrixModule This class define a class that allow to create a Cell Ranger matrix from an existing matrix file.MaxByteInputStream This class allow to create an InputStream that can read a maximum of byte from another InputStream.MergeInputRepLocalModule This class merges SAM files of input of the same experiment.MergePeaksModule This class defines the peak merging step.Merger This interface define a splitter.MergerModule This class define a generic merger module.Metadata This interface defines common methods for metadata.Minimap2IndexGeneratorModule This class define a module that generate a Minimap2 mapper index.Module This interface define a Module.ModuleRegistry This class define a registry for modules.Modules This class contains useful methods for writing Step classes.ModulesAction This class define an action that show the list of available formats.ModuleService This class allow to get a Step object from a class in the classpath.MonoThreadTaskScheduler This class define a mono thread scheduler.MultiQCModule This class define a module for MultiQC.MultiThreadTaskScheduler This class define a muti thread scheduler.Naming This class contains methods to validate workflow object names.NoLog This annotation is used to mark a step class that requires no log.NoOutputDirectory This annotation is used to mark a step class that requires no output directory.Normalization This class create and launch an R script to compute normalisation of expression dataNormalizationModule This class define the module for normalizationNoUI This class define an UI that do nothing.OtherLogConfigurator This class allow to configure non Eoulsan log using Log4J.OutputPort This interface define an output port of a step.OutputPorts This interface define a group of output ports.OutputPortsBuilder This class allow to easily create input ports for a step.PairedEndFastqToTfq This class allow to convert two FASTQ file in one TFQ file.PairedEndFastqToTfq.FastqPairedEndReducer This class define the reducer required to convert FASTQ files into TFQ file.ParallelizationMode This enum define the parallelization modes of a step.Parameter This class define a parameter.PathConcatInputStream This class define an InputStream that concatenate path in an InputStream.PathDataProtocol This class define an abstract class for DataProtocols based on the Hadoop framework Path object.PathRequirement This class define a executable requirement.PathUtils This class define utility method to manipulate the Hadoop Path object.PathUtils.PrefixPathFilter Simple PathFilter to filter Paths with their beginningPathUtils.SuffixPathFilter Simple PathFilter to filter Paths with their suffixPausableThreadPoolExecutor This class define a Pausable thread pool executor.PBSProTaskScheduler This class define a PBSPro cluster scheduler using a Bpipe script.Port This interface define a port of a step.Ports<E extends Port> This interface define a group of ports.PreTreatmentExpressionMapper This class define a mapper for the pretreatment of paired-end data before the expression estimation step.PreTreatmentExpressionReducer This class define a reducer for the pretreatment of paired-end data before the expression estimation step.PreTreatmentMapper This class defines a mapper for the pretreatment of paired-end data before the reads filtering step.PreTreatmentReducer This class define a reducer for the pretreatment of paired-end data before the reads filtering step.ProcessRExecutor This class define a standard RExecutor using a system process.ProcessUtils Utility class for launching external process.ProcessUtils.ProcessResult ProcessUtils.ProcessThreadErrOutput This class allow to fetch standard error of the process, without printingProgress This interface allow to set the progress of a task.ProgressCounterInputStream This class implements a FilterInputStream that inform Hadoop of the progress of task using counters.ProgressCounterOutputStream This class implements an OutputStream that inform Hadoop of the progress of task using counters.ReadsChecker This class define a checker on FASTQ files.ReadsFilterHadoopModule This class is the main class for the filter reads program in hadoop mode.ReadsFilterLocalModule This class define a module for reads filtering.ReadsFilterMapper This class defines a read filter mapper.ReadsMapperHadoopModule This class define an mapper module in Hadoop mode.ReadsMapperLocalModule This class define a module for reads mapping.ReadsMapperMapper This class defines a generic mapper for reads mapping.Requirement This interface define a requirement for an Eoulsan Step.RequirementInstallerModule This class allow to install a requirement.RequirementService This class define a service for requirements.RequiresAllPreviousSteps This annotation is used to mark a step class that requires the all the previous step in the workflow file.RequiresPreviousStep This annotation is used to mark a step class that requires the previous step in the workflow file.ResourceLoader<S> This interface define a resource loader.ReuseModuleInstance This annotation is used to mark a module class that can reuse a module instance for each task.RExecutor This interface define how to prepare, launch and retrieve data of a R analysis.RExecutorFactory This class define a factory to create RExecutor objects.RExecutorFactory.Mode Define a enum for the mode of RExecutor.RmDupLocalModule This class removes PCR duplicates from a SAM file.RModuleCommonConfiguration This class define common methods used for the configuration of the step of the package.RSConnection This class define an enhanced connection to RServe.RserveRequirement This class define a Rserve server requirement.RserveRExecutor This class define a RServe RExecutor.RSingleCellExperimentCreatorModule This class define a class that allow to create a SingleCellExperiment Bioconductor Object and save it as a RDS file.SAM2BAMHadoopModule This class define a module for converting SAM files into BAM.SAM2BAMLocalModule This class define a module for converting SAM files into BAM.SAM2FASTQLocalModule This class define a module for converting SAM files into FASTQ.SAMFilterHadoopModule This class define a filter alignment step in Hadoop mode.SAMFilterLocalModule This class define a Step for alignments filtering.SAMFilterMapper This class defines a mapper for alignment filtering.SAMFilterReducer This class define a reducer for alignments filtering.SAMHeaderHadoopUtils This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.SAMHeaderHadoopUtils.SAMHeaderWriter This class allow to save the SAM header read by a mapper.SAMInputFormat This class define an InputFormat for SAM files for the Hadoop MapReduce framework.SAMMerger This class define a merger class for SAM files.SAMOutputFormat This class define a SAM output format.Sample This interface defines a sample.SampleMetadata This interface defines the sample metadata.SAMRecordReader This class define a RecordReader for SAM files for the Hadoop MapReduce framework.SAMRecordWriter This class define a RecordWriter for SAM files.SAMSequenceFile This class define a SequenceFile for SAM files.SAMSplitter This class define a splitter class for SAM files.SelectParameterToolElement This class define a select tool element parameter.SerializableStopwatch Settings This class define a settings class.ShellModule This class define a module that execute a shell command.SimpleInputPort This class define an input port of a step.SimpleInputPorts This class define a class that handles a set of input ports.SimpleOutputPort This class define an output port of a step.SimpleOutputPorts This class define a class that contains several output ports.SLURMTaskScheduler This class define a SLURM cluster scheduler using a Bpipe script.Splice2BEDModule This class define a module for converting SAM files into BED.Splitter This interface define a splitter.SplitterModule This class define a generic splitter module.STARIndexGeneratorModule This class define a module that generate a STAR mapper index.Step This interface define a step of the workflow.Step.DiscardOutput This enum define the value of the discard output attribute of the step tag in the Eoulsan workflow file.Step.StepState This enum define the states of the steps.Step.StepType This enum define the type of step.StepConfigurationContext StepConfigurationContextImpl This class define a concrete implementation of the configuration context of a step.StepInstances This class store module instances and avoid storing this instance in Step objects that are serialized.StepObserver This interface define workflow step eventsStepObserverRegistry This class allow to relay workflow step events to other observers.StepOutputDataFile This class define an output file of workflow set.StepResult This class define a step result.StepStateDependencies This class allow to store the step state and its dependencies.StepStatus This class define a step status.StorageDataProtocol This abstract class define a storage protocol.TaskContext This interface define the context of a step.TaskContextImpl This class define a task context.TaskResult This class define the result of a step.TaskResultImpl This class define a result for a task context.TaskRunner This class allow to run a task context.TaskScheduler This interface define a task scheduler.TaskSchedulerFactory This class define a factory for TaskScheduler that can create only one instance.TaskSerializationUtils This class contains utility methods for serialization, deserialization and execution of Task objects.TaskStatus This interface define a step status.TaskStatusImpl This class define a task status.TechnicalReplicateMergerModule This class define a merger module for technical replicates.Terminal This annotation is used to mark a step class that is a terminal step.TerminalModule This class define a terminal task that do nothing.TextParameterToolElement This class define a text tool element parameter.TGCCTaskScheduler This class define a TGCC cluster scheduler.Ticket This class define a ticket for the TicketLocker.TicketLocker This class define a global locker using RMI messaging.TicketScheduler Define the rmi interface for the TicketSchedulerServer.TicketSchedulerServer This class define a server for the scheduler.TokenManager This class define a token manager for a step.TokenManagerRegistry This class store all the TokenManager instances.ToolElement The ToolElement interface.ToolElementFactory This class define a factory for ToolElement objects.ToolExecutor The class define an executor on tool set in XML file.ToolExecutorResult The class define a result on execution tool.ToolInfo The class define a tool data which contains all data extracted from XML file.TORQUETaskScheduler This class define a TORQUE cluster scheduler using a Bpipe script.TrackHubModule This class construct TrackHub for genome browser visualization.UI This interface define how UI is informed of The workflow changes.UIEvent This class define an abstract UIEventUIService This class define a service to retrieve a UI.UIStepEvent This class define a UI step event.UITaskEvent This class define a UI task event.UIWorkflowEvent This class define a UI workflow event.UnmodifiableData This class define an unmodifiable dataUnmodifiableExperiment UnmodifiableExperimentMetadata UnmodifiableExperimentSampleMetadata UploadModule This class define a abstract module class for files uploading.URLDataProtocol This class define an abstract class for DataProtocols based on the URL class.Utils Workflow This interface define a Workflow.Workflow2Graphviz Convert a Workflow to GraphvizWorkflowContext This class define the context implementation.WorkflowDataUtils This class define an utility on data object.WorkflowEventBus This class define a single for the event bus.WorkflowFileNaming This class contains methods to create workflow data file names.XMLDataFormat This class define a DataFormat from an XML file.ZooKeeperLocker This class implements a locker using Zookeeper.