Class MACS2Module
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
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- fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
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- All Implemented Interfaces:
Module
public class MACS2Module extends AbstractModule
This class defines the macs2 peak-calling step. Handle multiple experiments with one control per experiment.- Author:
- Pierre-Marie Chiaroni - CSB lab - ENS - Paris, Celine Hernandez - CSB lab - ENS - Paris, Cedric Michaud - CSB lab - ENS - Paris
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Field Summary
Fields Modifier and Type Field Description protected static String
COUNTER_GROUP
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Constructor Summary
Constructors Constructor Description MACS2Module()
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Method Summary
All Methods Instance Methods Concrete Methods 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 macs2.String
getDescription()
Get the description of the moduleInputPorts
getInputPorts()
Get the input data format.String
getName()
Get the name of the module.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
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Field Detail
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COUNTER_GROUP
protected static final String COUNTER_GROUP
- See Also:
- Constant Field Values
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Method Detail
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getName
public String getName()
Description copied from interface:Module
Get the name of the module.- Returns:
- the name of the module
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getDescription
public String getDescription()
Description copied from interface:Module
Get the description of the module- Specified by:
getDescription
in interfaceModule
- Overrides:
getDescription
in classAbstractModule
- Returns:
- the description of the module
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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
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getInputPorts
public InputPorts getInputPorts()
Description copied from interface:Module
Get the input data format.- Specified by:
getInputPorts
in interfaceModule
- Overrides:
getInputPorts
in classAbstractModule
- Returns:
- a set with DataFormat or null if the module does not any need input format
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getOutputPorts
public OutputPorts getOutputPorts()
Description copied from interface:Module
Get the output data format.- Specified by:
getOutputPorts
in interfaceModule
- Overrides:
getOutputPorts
in classAbstractModule
- Returns:
- an set with DataFormat or null if the module does not produce any output data
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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 interfaceModule
- Overrides:
configure
in classAbstractModule
- Parameters:
stepParameters
- parameters of the stepcontext
- configuration context. The context can be null for generator steps- Throws:
EoulsanException
- if a parameter is invalid
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getRequirements
public Set<Requirement> getRequirements()
Description copied from interface:Module
Get the requirements of the module.- Specified by:
getRequirements
in interfaceModule
- Overrides:
getRequirements
in classAbstractModule
- Returns:
- a set with the requirements of the module
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execute
public TaskResult execute(TaskContext context, TaskStatus status)
Run macs2.- Parameters:
context
- Execution contextstatus
- of the task
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