Package fr.ens.biologie.genomique.eoulsan.modules.diffana

Class DESeq2Module

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module

All Implemented Interfaces:

Module

public class DESeq2Module
extends AbstractModule

Class to run the differential analysis with DEseq2

Since:

2.0

Author:

Xavier Bauquet

Field Summary

Fields

Modifier and Type	Field	Description
static String	MODULE_NAME

Constructor Summary

Constructors

Constructor	Description
DESeq2Module()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
Checker	getChecker()	Get the checker for the module
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
Set<Requirement>	getRequirements()	Get the requirements of the module.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getDescription, getOutputPorts, getParallelizationMode, getRequiredEoulsanVersion

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MODULE_NAME

public static final String MODULE_NAME

See Also:

Constant Field Values

Constructor Detail

DESeq2Module

public DESeq2Module()

Method Detail

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getVersion

public fr.ens.biologie.genomique.kenetre.util.Version getVersion()

Description copied from interface: Module

Get version of the Module.

Returns:

a Version object with the version of the Module

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

a set with DataFormat or null if the module does not any need input format

getRequirements

public Set<Requirement> getRequirements()

Description copied from interface: Module

Get the requirements of the module.

Specified by:

getRequirements in interface Module

Overrides:

getRequirements in class AbstractModule

Returns:

a set with the requirements of the module

getChecker

public Checker getChecker()

Description copied from interface: Module

Get the checker for the module

Specified by:

getChecker in interface Module

Overrides:

getChecker in class AbstractModule

Returns:

the checker for the module

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task