Uses of Class
fr.ens.biologie.genomique.eoulsan.core.Parameter

Packages that use Parameter

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.galaxytools	This package contain classes related to read tool xml file from galaxy.
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.chipseq.peakcalling	This packages contains the peak-calling modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc	This packages contains all the quality check modules for ChIP-Seq.
fr.ens.biologie.genomique.eoulsan.modules.diffana	This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.modules.expression	This package contain all the classes related to the expression step.
fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop	This package contain all the classes related to the expression step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.fastqc	This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators	This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop	This package contain classes related data management in Hadoop mode.
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.modules.singlecell
fr.ens.biologie.genomique.eoulsan.requirements	This package contains requirement classes for Eoulsan.
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 Parameter in fr.ens.biologie.genomique.eoulsan.checkers

Method parameters in fr.ens.biologie.genomique.eoulsan.checkers with type arguments of type Parameter

Modifier and Type	Method	Description
void	Checker.configure(Set<Parameter> stepParameters)	Set the parameters of the checker to configure the checker.
void	DESeq2DesignChecker.configure(Set<Parameter> stepParameters)
void	GenomeChecker.configure(Set<Parameter> stepParameters)
void	GFFChecker.configure(Set<Parameter> stepParameters)
void	ReadsChecker.configure(Set<Parameter> stepParameters)

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

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

Modifier and Type	Method	Description
static Parameter	Modules.getParameter(Set<Parameter> parameters, String parameterName)	Get the last parameter which name match for a parameter set.

Methods in fr.ens.biologie.genomique.eoulsan.core that return types with arguments of type Parameter

Modifier and Type	Method	Description
Set<Parameter>	Step.getParameters()	Get the parameter of the step.

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

Modifier and Type	Method	Description
static void	Modules.badParameterValue(StepConfigurationContext context, Parameter parameter, String message)	Throw a exception for bad parameter value.
static void	Modules.badParameterValue(String stepId, Parameter parameter, String message)	Throw a exception for bad parameter value.
int	Parameter.compareTo(Parameter p)
static void	Modules.deprecatedParameter(StepConfigurationContext context, Parameter parameter)	Show a message for deprecated parameters.
static void	Modules.deprecatedParameter(StepConfigurationContext context, Parameter parameter, boolean throwException)	Show a message for deprecated parameters.
static void	Modules.deprecatedParameter(String stepId, Parameter parameter, boolean throwException)	Show a message for deprecated parameters.
static void	Modules.removedParameter(StepConfigurationContext context, Parameter parameter)	Throw a exception for removed parameters.
static void	Modules.removedParameter(String stepId, Parameter parameter)	Throw a exception for removed parameters.
static void	Modules.renamedParameter(StepConfigurationContext context, Parameter parameter, String newParameterName)	Show a message for deprecated parameters that has been renamed.
static void	Modules.renamedParameter(StepConfigurationContext context, Parameter parameter, String newParameterName, boolean throwException)	Show a message for deprecated parameters that has been renamed.
static void	Modules.renamedParameter(String stepId, Parameter parameter, String newParameterName, boolean throwException)	Show a message for deprecated parameters that has been renamed.
static void	Modules.unknownParameter(StepConfigurationContext context, Parameter parameter)	Throw a exception for unknown parameters.
static void	Modules.unknownParameter(String stepId, Parameter parameter)	Throw a exception for unknown parameters.

Method parameters in fr.ens.biologie.genomique.eoulsan.core with type arguments of type Parameter

Modifier and Type	Method	Description
void	Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
static boolean	Modules.containsParameter(Set<Parameter> parameters, String parameterName)	test if a set of parameters contains a parameter.
static Parameter	Modules.getParameter(Set<Parameter> parameters, String parameterName)	Get the last parameter which name match for a parameter set.

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

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that return types with arguments of type Parameter

Modifier and Type	Method	Description
Set<Parameter>	CommandWorkflowModel.getGlobalParameters()	Get the globals parameters.
Set<Parameter>	AbstractStep.getParameters()
Set<Parameter>	CommandWorkflowModel.getStepParameters(String stepId)	Get the parameters of a step

Constructor parameters in fr.ens.biologie.genomique.eoulsan.core.workflow with type arguments of type Parameter

Constructor	Description
CommandStep(AbstractWorkflow workflow, Module module, Set<Parameter> parameters)	Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct)	Create a step for a standard step.
CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct, DataFile outputDirectory)	Create a step for a standard step.

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.galaxytools

Method parameters in fr.ens.biologie.genomique.eoulsan.galaxytools with type arguments of type Parameter

Modifier and Type	Method	Description
void	GalaxyToolInterpreter.configure(Set<Parameter> parameters)	Parse tool file to extract useful data to run tool.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractConditionalParamElement(ToolInfo toolInfo, Element parent, Map<String,Parameter> stepParameters)	Extract conditional param element.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractInputs(ToolInfo toolInfo, Document doc, Map<String,Parameter> stepParameters)	Extract all input parameters define in document.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractOutputs(ToolInfo toolInfo, Document doc, Map<String,Parameter> stepParameters)	Extract all output parameters define in document.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractParamElement(ToolInfo toolInfo, Element parent, String elementName, Map<String,Parameter> stepParameters)	Extract parameter elements.
static void	GalaxyToolXMLParserUtils.setElementValue(ToolElement toolElement, Map<String,Parameter> stepParameters)	Set the tool element value.

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

Method parameters in fr.ens.biologie.genomique.eoulsan.galaxytools.elements with type arguments of type Parameter

Modifier and Type	Method	Description
void	ConditionalToolElement.setValues(Map<String,Parameter> stepParameters)	Set the values.

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

Method parameters in fr.ens.biologie.genomique.eoulsan.modules with type arguments of type Parameter

Modifier and Type	Method	Description
void	AbstractModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	CopyInputDataModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	CopyOutputDataModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DesignModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	FailModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	FakeModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	GalaxyToolModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ImportModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	MergerModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	RequirementInstallerModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ShellModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	SplitterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
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 Parameter in fr.ens.biologie.genomique.eoulsan.modules.chipseq

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.chipseq with type arguments of type Parameter

Modifier and Type	Method	Description
void	MergeInputRepLocalModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	RmDupLocalModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	TrackHubModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling with type arguments of type Parameter

Modifier and Type	Method	Description
void	BedToolsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	DeepToolsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	MACS2Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	MergePeaksModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc with type arguments of type Parameter

Modifier and Type	Method	Description
void	CountSplicedReadsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	IDRModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set IDR parameters to configure the step.

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.diffana

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

Modifier and Type	Method	Description
static DESeq2.SizeFactorsType	DESeq2.SizeFactorsType.get(Parameter parameter)	Get the size factors type to be used in DESeq2.

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.diffana with type arguments of type Parameter

Modifier and Type	Method	Description
void	DESeq2Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DiffAnaModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DiffanaResultsAnnotationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	NormalizationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
static RExecutor	RModuleCommonConfiguration.parseRExecutorParameter(StepConfigurationContext context, Set<Parameter> stepParameters, Set<Requirement> requirements, String defaultDockerImage)	Parse the step parameter and create a configured RExecutor object.

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.expression

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.expression with type arguments of type Parameter

Modifier and Type	Method	Description
void	AbstractExpressionModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ExpressionResultsAnnotationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop with type arguments of type Parameter

Modifier and Type	Method	Description
void	ExpressionHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.fastqc

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.fastqc with type arguments of type Parameter

Modifier and Type	Method	Description
void	FastQCModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.generators

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.generators with type arguments of type Parameter

Modifier and Type	Method	Description
void	GenericStorageGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	GenomeMapperIndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	Minimap2IndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	STARIndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.mapping

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.mapping with type arguments of type Parameter

Modifier and Type	Method	Description
void	AbstractBAM2SAMModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractFilterAndMapReadsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractReadsFilterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractReadsMapperModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAM2BAMModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAM2FASTQModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAMFilterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSplice2BEDModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop with type arguments of type Parameter

Modifier and Type	Method	Description
void	FilterAndMapReadsHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ReadsMapperHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop with type arguments of type Parameter

Modifier and Type	Method	Description
void	CopyDesignAndWorkflowFilesToOutputModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

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

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload with type arguments of type Parameter

Modifier and Type	Method	Description
void	DefineDataFormatToDownload.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	HDFSDataDownloadModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

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

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.multiqc with type arguments of type Parameter

Modifier and Type	Method	Description
void	MultiQCModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.modules.singlecell

Method parameters in fr.ens.biologie.genomique.eoulsan.modules.singlecell with type arguments of type Parameter

Modifier and Type	Method	Description
void	ExpressionToMatrixModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	MatrixToCellRangerMatrixModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	RSingleCellExperimentCreatorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of Parameter in fr.ens.biologie.genomique.eoulsan.requirements

Methods in fr.ens.biologie.genomique.eoulsan.requirements that return types with arguments of type Parameter

Modifier and Type	Method	Description
Set<Parameter>	AbstractRequirement.getParameters()
Set<Parameter>	DockerRequirement.getParameters()
Set<Parameter>	PathRequirement.getParameters()
Set<Parameter>	Requirement.getParameters()	Get the parameters of the requirement
Set<Parameter>	RserveRequirement.getParameters()

Method parameters in fr.ens.biologie.genomique.eoulsan.requirements with type arguments of type Parameter

Modifier and Type	Method	Description
void	AbstractRequirement.configure(Set<Parameter> parameters)
void	DockerRequirement.configure(Set<Parameter> parameters)
void	PathRequirement.configure(Set<Parameter> parameters)
void	Requirement.configure(Set<Parameter> parameters)	Configure the requirement.
void	RserveRequirement.configure(Set<Parameter> parameters)

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

Method parameters in fr.ens.biologie.genomique.eoulsan.splitermergers with type arguments of type Parameter

Modifier and Type	Method	Description
void	BAMMerger.configure(Set<Parameter> conf)
void	BAMSplitter.configure(Set<Parameter> conf)
void	ExpressionMerger.configure(Set<Parameter> conf)
void	ExpressionSplitter.configure(Set<Parameter> conf)
void	FastqMerger.configure(Set<Parameter> conf)
void	FastqSplitter.configure(Set<Parameter> conf)
void	Merger.configure(Set<Parameter> conf)	Configure the merger.
void	SAMMerger.configure(Set<Parameter> conf)
void	SAMSplitter.configure(Set<Parameter> conf)
void	Splitter.configure(Set<Parameter> conf)	Configure the splitter.