Class DeepToolsModule
- 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.DeepToolsModule
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- All Implemented Interfaces:
Module
public class DeepToolsModule extends AbstractModule
This class uses tools from the DeepTools suite.- Author:
- Celine Hernandez - CSB lab - ENS - Paris, Cedric Michaud - CSB lab - ENS - Paris
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Constructor Summary
Constructors Constructor Description DeepToolsModule()
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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 deeptools.String
getDescription()
Get the description of the moduleInputPorts
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
getChecker, getOutputPorts, getParallelizationMode, getRequiredEoulsanVersion
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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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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 deeptools.- Parameters:
context
- Execution contextstatus
- of the task
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