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

Class BedToolsModule

java.lang.Object

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

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

All Implemented Interfaces:

Module

public class BedToolsModule
extends AbstractModule

This class uses tools from the BEDTools suite.

Author:

Celine Hernandez - CSB lab - ENS - Paris

Constructor Summary

Constructors

Constructor	Description
BedToolsModule()

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)	Run bedtools multiinter.
String	getDescription()	Get the description of the module
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Methods
OutputPorts	getOutputPorts()	Get the output data format.
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

getChecker, getParallelizationMode, getRequiredEoulsanVersion

Methods inherited from class java.lang.Object

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

Constructor Detail

BedToolsModule

public BedToolsModule()

Method Detail

getName

public String getName()

Methods

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

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractModule

Returns:

an set with DataFormat or null if the module does not produce any output data

configure

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

Set the parameters of the step to configure the 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

Throws:

EoulsanException - if a parameter is invalid

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

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Run bedtools multiinter. Installation (if needed) was made during configuration.

Parameters:

context - Execution context

status - of the task