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

Class IDRModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule

All Implemented Interfaces:

Module

public class IDRModule
extends AbstractModule

This class defines the IDR quality check step. This QC step determines the reproducibility of peaks between replicates.

Author:

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

Constructor Summary

Constructors

Constructor	Description
IDRModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set IDR parameters to configure the step.
TaskResult	execute(TaskContext context, TaskStatus status)	Install all the files necessary in the tmp folder, then run idr.
String	getDescription()	A short description of the tool and what is done in the step.
InputPorts	getInputPorts()	Define input ports.
String	getName()	Name of the Step.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Version.

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

IDRModule

public IDRModule()

Method Detail

getName

public String getName()

Name of the Step.

Returns:

the name of the module

getDescription

public String getDescription()

A short description of the tool and what is done in the step.

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()

Version.

Returns:

a Version object with the version of the Module

getInputPorts

public InputPorts getInputPorts()

Define input ports.

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)
               throws EoulsanException

Set IDR parameters to configure the step. As written in IDR documentation, concerning parameter peak.half.width : "IMPORTANT: Currrently this parameter does not work properly so please pre-truncate your peaks if desired before feeding to IDR. Always set this parameter to -1."

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

context - step configuration context

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Install all the files necessary in the tmp folder, then run idr.

Parameters:

context - Execution context

status - of the task