Package fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling

Class MergePeaksModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule

All Implemented Interfaces:

Module

public class MergePeaksModule
extends AbstractModule

This class defines the peak merging step. It merges peak files created by a peak caller into one BED file.

Author:

Pierre-Marie Chiaroni - CSB lab - ENS - Paris, Celine Hernandez - CSB lab - ENS - Paris

Constructor Summary

Constructors

Constructor	Description
MergePeaksModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
String	getDescription()	Get the description of the module
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name 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

getChecker, getOutputPorts, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

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

Constructor Detail

MergePeaksModule

public MergePeaksModule()

Method Detail

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getDescription

public String getDescription()

Description copied from interface: Module

Get the description of the module

Specified by:

getDescription in interface Module

Overrides:

getDescription in class AbstractModule

Returns:

the description 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

configure

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

Set the parameters of the step to configure the step. Nothing to configure for such a simple step.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

stepParameters - parameters of the step

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

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