Uses of Interface
fr.ens.biologie.genomique.eoulsan.data.DataFormat

Packages that use DataFormat

Package	Description
fr.ens.biologie.genomique.eoulsan.checkers	This package contains and define checkers of DataFormat.
fr.ens.biologie.genomique.eoulsan.core	This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.workflow	This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.data	This package contains classes for data files, data types and data formats.
fr.ens.biologie.genomique.eoulsan.galaxytools.elements	This package contain classes related to parameter extractions from XML Galaxy tool xml files.
fr.ens.biologie.genomique.eoulsan.modules	This package define the steps for the Eoulsan workflow.
fr.ens.biologie.genomique.eoulsan.modules.chipseq	This packages contains the ChIP-Seq modules.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload	This package contain classes related to upload data to HDFS and Cloud.
fr.ens.biologie.genomique.eoulsan.modules.multiqc
fr.ens.biologie.genomique.eoulsan.splitermergers	This package contains splitter and merger used when running Eoulsan on a standard cluster to get more parallelization efficiency.

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.checkers

Methods in fr.ens.biologie.genomique.eoulsan.checkers that return DataFormat

Modifier and Type	Method	Description
DataFormat	Checker.getFormat()	Get format related to the checker.
DataFormat	DESeq2DesignChecker.getFormat()
DataFormat	GenomeChecker.getFormat()
DataFormat	GFFChecker.getFormat()
DataFormat	ReadsChecker.getFormat()

Methods in fr.ens.biologie.genomique.eoulsan.checkers that return types with arguments of type DataFormat

Modifier and Type	Method	Description
Set<DataFormat>	Checker.getCheckersRequired()	Get the list of Checker required to run before this checker.
Set<DataFormat>	DESeq2DesignChecker.getCheckersRequired()
Set<DataFormat>	GenomeChecker.getCheckersRequired()
Set<DataFormat>	GFFChecker.getCheckersRequired()
Set<DataFormat>	ReadsChecker.getCheckersRequired()

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.core

Methods in fr.ens.biologie.genomique.eoulsan.core that return DataFormat

Modifier and Type	Method	Description
DataFormat	AbstractPort.getFormat()
DataFormat	FileNaming.getFormat()	Get the format.
DataFormat	Port.getFormat()	Get the data format of the port.

Methods in fr.ens.biologie.genomique.eoulsan.core with parameters of type DataFormat

Modifier and Type	Method	Description
InputPortsBuilder	InputPortsBuilder.addPort(String name, boolean list, DataFormat format)	Add an input port.
InputPortsBuilder	InputPortsBuilder.addPort(String name, boolean list, DataFormat format, boolean requiredInWorkingDirectory)	Add an input port.
InputPortsBuilder	InputPortsBuilder.addPort(String name, boolean list, DataFormat format, EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted)	Add an input port.
InputPortsBuilder	InputPortsBuilder.addPort(String name, boolean list, DataFormat format, EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted, boolean requiredInWorkingDirectory)	Add an input port.
InputPortsBuilder	InputPortsBuilder.addPort(String name, DataFormat format)	Add an input port.
InputPortsBuilder	InputPortsBuilder.addPort(String name, DataFormat format, boolean requiredInWorkingDirectory)	Add an input port.
InputPortsBuilder	InputPortsBuilder.addPort(String name, DataFormat format, EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted)	Add an input port.
InputPortsBuilder	InputPortsBuilder.addPort(String name, DataFormat format, EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted, boolean requiredInWorkingDirectory)	Add an input port.
OutputPortsBuilder	OutputPortsBuilder.addPort(String name, boolean list, DataFormat format)	Add an output port.
OutputPortsBuilder	OutputPortsBuilder.addPort(String name, boolean list, DataFormat format, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Add an output port.
OutputPortsBuilder	OutputPortsBuilder.addPort(String name, DataFormat format)	Add an output port.
OutputPortsBuilder	OutputPortsBuilder.addPort(String name, DataFormat format, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Add an output port.
int	AbstractPorts.countDataFormat(DataFormat format)
int	Ports.countDataFormat(DataFormat format)	Count the number of occurrences of a format in the port.
static String	FileNaming.filename(String stepId, String portName, DataFormat format, String dataName, int fileIndex, int part, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Create the filename from several parameters.
static String	FileNaming.filePrefix(String stepId, String portName, DataFormat format)	Create the prefix of a filename.
static String	FileNaming.fileSuffix(DataFormat format, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Create the suffix of a file.
Data	TaskContext.getInputData(DataFormat format)	Get the input data for an input DataType and a Sample.
Data	TaskContext.getOutputData(DataFormat format, Data origin)	Get the output data for an input DataType and a Sample.
Data	TaskContext.getOutputData(DataFormat format, String dataName)	Get the output data for an input DataType and a Sample.
Data	TaskContext.getOutputData(DataFormat format, String dataName, int part)	Get the output data for an input DataType and a Sample.
List<E>	AbstractPorts.getPortsWithDataFormat(DataFormat format)
List<E>	Ports.getPortsWithDataFormat(DataFormat format)	Get a list with all the ports that format is the specified format.
void	FileNaming.setFormat(DataFormat format)	Set the format.
static InputPorts	InputPortsBuilder.singleInputPort(DataFormat format)	Convenient method to create the ports with only one port.
static InputPorts	InputPortsBuilder.singleInputPort(String name, DataFormat format)	Convenient method to create the ports with only one port.
static OutputPorts	OutputPortsBuilder.singleOutputPort(DataFormat format)	Convenient method to create the ports with only one port.
static OutputPorts	OutputPortsBuilder.singleOutputPort(String name, DataFormat format)	Convenient method to create the ports with only one port.

Constructors in fr.ens.biologie.genomique.eoulsan.core with parameters of type DataFormat

Constructor	Description
SimpleInputPort(String name, boolean list, DataFormat format, EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted, boolean requiredInWorkingDirectory)	Constructor.
SimpleInputPort(String name, DataFormat format, EnumSet<fr.ens.biologie.genomique.kenetre.io.CompressionType> compressionsAccepted, boolean requiredInWorkingDirectory)	Constructor.
SimpleOutputPort(String name, boolean list, DataFormat format, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Constructor.
SimpleOutputPort(String name, DataFormat format, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Constructor.

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.core.workflow

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return DataFormat

Modifier and Type	Method	Description
DataFormat	StepOutputDataFile.getFormat()	Get the format of the output
DataFormat	UnmodifiableData.getFormat()

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type DataFormat

Modifier and Type	Method	Description
Data	TaskContextImpl.getInputData(DataFormat format)
Data	TaskContextImpl.getOutputData(DataFormat format, Data origin)
Data	TaskContextImpl.getOutputData(DataFormat format, String dataName)
Data	TaskContextImpl.getOutputData(DataFormat format, String dataName, int part)
static String	StepOutputDataFile.newStandardFilename(Step step, String portName, DataFormat format, Sample sample, int fileIndex, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Create a standard filename.

Constructors in fr.ens.biologie.genomique.eoulsan.core.workflow with parameters of type DataFormat

Constructor	Description
CommandStep(AbstractWorkflow workflow, DataFormat format)	Create a Generator Workflow step.

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.data

Classes in fr.ens.biologie.genomique.eoulsan.data that implement DataFormat

Modifier and Type	Class	Description
class	MapperIndexDataFormat	This class define a DataFormat from an XML file.
class	XMLDataFormat	This class define a DataFormat from an XML file.

Fields in fr.ens.biologie.genomique.eoulsan.data declared as DataFormat

Modifier and Type	Field	Description
static DataFormat	DataFormats.ADDITIONAL_ANNOTATION_TSV	Additional annotation data format.
static DataFormat	DataFormats.ANNOTATED_EXPRESSION_RESULTS_ODS	ODS Annotated expression results data format.
static DataFormat	DataFormats.ANNOTATED_EXPRESSION_RESULTS_TSV	TSV Annotated expression results data format.
static DataFormat	DataFormats.ANNOTATED_EXPRESSION_RESULTS_XLSX	XLSX Annotated expression results data format.
static DataFormat	DataFormats.ANNOTATION_GFF	GFF data format.
static DataFormat	DataFormats.ANNOTATION_GTF	GTF data format.
static DataFormat	DataFormats.BIGBED	BigBed format.
static DataFormat	DataFormats.BIGWIG	BigWig format.
static DataFormat	DataFormats.BOWTIE_INDEX_ZIP	Bowtie index data format.
static DataFormat	DataFormats.BOWTIE2_INDEX_ZIP	Bowtie2 index data format.
static DataFormat	DataFormats.BWA_INDEX_ZIP	BWA index data format.
static DataFormat	DataFormats.CUTADAPT_ADAPTER_FASTA	Cutadapt adapters format.
static DataFormat	DataFormats.DIFFANA_RESULTS_TSV	Diffana results data format.
static DataFormat	DataFormats.DUMMY_TXT	Dummy format.
static DataFormat	DataFormats.EXPRESSION_MATRIX_TSV	Expression matrix.
static DataFormat	DataFormats.EXPRESSION_RESULTS_TSV	Expression results data format.
static DataFormat	DataFormats.FASTQC_REPORT_HTML	FastQC HTML report format.
static DataFormat	DataFormats.FASTQC_REPORT_ZIP	FastQC ZIP report format.
static DataFormat	DataFormats.FEATURECOUNTS_SUMMARY_TXT	FeatureCounts summary format.
static DataFormat	DataFormats.GENOME_DESC_TXT	Genome data format.
static DataFormat	DataFormats.GENOME_FASTA	Genome data format.
static DataFormat	DataFormats.GSNAP_INDEX_ZIP	Gmap index data format.
static DataFormat	DataFormats.MAPPER_RESULT_BED	BED format.
static DataFormat	DataFormats.MAPPER_RESULTS_BAM	BAM results data format.
static DataFormat	DataFormats.MAPPER_RESULTS_INDEX_BAI	BAM index results data format.
static DataFormat	DataFormats.MAPPER_RESULTS_LOG	Mapper log file format.
static DataFormat	DataFormats.MAPPER_RESULTS_SAM	SAM results data format.
static DataFormat	DataFormats.MINIMAP2_INDEX_ZIP	Minimap2 index data format.
static DataFormat	DataFormats.MULTIQC_REPORT_HTML	MultiQC HTML report format.
static DataFormat	DataFormats.READS_FASTQ	Reads fastq data format.
static DataFormat	DataFormats.READS_TFQ	Reads tfq data format.
static DataFormat	DataFormats.SINGLE_CELL_EXPERMIMENT_RDS	R single cell experiment.
static DataFormat	DataFormats.STAR_INDEX_ZIP	STAR index data format.
static DataFormat	DataFormats.UNMAP_READS_FASTA	Unmap reads results data format.

Methods in fr.ens.biologie.genomique.eoulsan.data that return DataFormat

Modifier and Type	Method	Description
DataFormat	DataFile.getDataFormat()	Get the DataFormat of the DataFile.
DataFormat	DataFileMetadata.getDataFormat()	Get the DataFormat of the file.
DataFormat	DataFormatRegistry.getDataFormatForDesignMetadata(String key)	Get the DataFormat that define a metadata entry in the design file.
DataFormat	DataFormatRegistry.getDataFormatForSampleMetadata(String key)	Get the DataFormat that define a metadata entry of a sample in the design file.
DataFormat	DataFormatRegistry.getDataFormatFromAlias(String dataFormatAlias)	Get a DataFormat from its alias.
DataFormat	DataFormatRegistry.getDataFormatFromFilename(String filename)	Get the DataFormat of a file from its filename
DataFormat	DataFormatRegistry.getDataFormatFromFilename(String prefix, String extension)	Get a DataFormat From a file prefix and extension
DataFormat	DataFormatRegistry.getDataFormatFromGalaxyFormatName(String formatName)	Get DataFormat from an Galaxy format name.
DataFormat	DataFormatRegistry.getDataFormatFromGalaxyFormatNameOrNameOrAlias(String name)	Get a DataFormat from its Galaxy format name or its name or alias.
DataFormat	DataFormatRegistry.getDataFormatFromName(String dataFormatName)	Get a DataFormat from its name.
DataFormat	DataFormatRegistry.getDataFormatFromNameOrAlias(String name)	Get a DataFormat from its alias.
DataFormat	Data.getFormat()	Get the data format of the data.

Methods in fr.ens.biologie.genomique.eoulsan.data that return types with arguments of type DataFormat

Modifier and Type	Method	Description
Set<DataFormat>	DataFormatRegistry.getAllFormats()	Get all the registered formats.
Set<DataFormat>	DataFormatRegistry.getDataFormatsFromExtension(String extension)	Get DataFormats from an extension.

Methods in fr.ens.biologie.genomique.eoulsan.data with parameters of type DataFormat

Modifier and Type	Method	Description
String	DataFormatRegistry.getDesignMetadataKeyForDataFormat(Design design, DataFormat dataformat)	Get the field name in a Design object that correspond to a dataformat.
String	DataFormatRegistry.getSampleMetadataKeyForDataFormat(Sample sample, DataFormat dataformat)	Get the field name in a Sample object that correspond to a dataformat.
void	DataFormatRegistry.register(DataFormat df)	Register a DataFormat.
void	DataFormatRegistry.register(DataFormat[] array)	Register DataFormats.

Constructors in fr.ens.biologie.genomique.eoulsan.data with parameters of type DataFormat

Constructor	Description
DataFormatConverter(DataFile inFile, DataFile outFile, DataFormat outFormat, OutputStream os)	Constructor

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.galaxytools.elements

Methods in fr.ens.biologie.genomique.eoulsan.galaxytools.elements that return DataFormat

Modifier and Type	Method	Description
DataFormat	DataToolElement.getDataFormat()	Get the data format of the tool element.

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.modules

Methods in fr.ens.biologie.genomique.eoulsan.modules with parameters of type DataFormat

Modifier and Type	Method	Description
static void	CheckerModule.configureChecker(DataFormat format, Set<Parameter> parameters)	This method allow to configure a checker from the configure method of other steps, that's why this method is static.

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.modules.chipseq

Fields in fr.ens.biologie.genomique.eoulsan.modules.chipseq declared as DataFormat

Modifier and Type	Field	Description
static DataFormat	ChIPSeqDataFormats.GAPPED_PEAK	Gapped peak format.
static DataFormat	ChIPSeqDataFormats.MACS2_RMODEL	MACS 2 R model format.
static DataFormat	ChIPSeqDataFormats.PEAK	Peak format data format.
static DataFormat	ChIPSeqDataFormats.PEAK_XLS	Peaks XLS format.

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with parameters of type DataFormat

Modifier and Type	Method	Description
protected DataFile	HadoopUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected DataFile	LocalUploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)
protected abstract DataFile	UploadModule.getUploadedDataFile(DataFile file, Step step, Sample sample, String portName, DataFormat format, int fileIndex)	Generate the DataFile Object for the uploaded DataFile

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.modules.multiqc

Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc that return DataFormat

Modifier and Type	Method	Description
DataFormat	ExpressionInputPreprocessor.getDataFormat()
DataFormat	FastQCInputPreprocessor.getDataFormat()
DataFormat	FeatureCountsInputPreprocessor.getDataFormat()
DataFormat	InputPreprocessor.getDataFormat()	Get the DataFormat handled by the preprocessor.
DataFormat	MapperInputPreprocessor.getDataFormat()

Uses of DataFormat in fr.ens.biologie.genomique.eoulsan.splitermergers

Methods in fr.ens.biologie.genomique.eoulsan.splitermergers that return DataFormat

Modifier and Type	Method	Description
DataFormat	BAMMerger.getFormat()
DataFormat	BAMSplitter.getFormat()
DataFormat	ExpressionMerger.getFormat()
DataFormat	ExpressionSplitter.getFormat()
DataFormat	FastqMerger.getFormat()
DataFormat	FastqSplitter.getFormat()
DataFormat	Merger.getFormat()	Get the format related to the splitter.
DataFormat	SAMMerger.getFormat()
DataFormat	SAMSplitter.getFormat()
DataFormat	Splitter.getFormat()	Get the format related to the splitter.