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 Details

    • BedToolsModule

      public BedToolsModule()

  • Method Details

    • 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
      Returns:
      a TaskResult object