Package fr.ens.biologie.genomique.aozan.aozan3.dataprocessor

Class ExternalTool

java.lang.Object

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.ExternalTool

public class ExternalTool
extends Object

This class define a class for calling external tool in DataProcessors.

Since:

3.0

Author:

Laurent Jourdren

Method Summary

Modifier and Type	Method	Description
String	getToolVersion(RunId runId, String tmpDirPath, List<String> commandLine, boolean parseStdErr, Function<List<String>,String> parser)	Get the tool executable version.
fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess	newSimpleProcess(RunId runId, boolean enableLogging)	Create a new process.

Methods inherited from class java.lang.Object

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

Method Detail

newSimpleProcess

public fr.ens.biologie.genomique.kenetre.util.process.SimpleProcess newSimpleProcess(RunId runId,
                                                                                     boolean enableLogging)
                                                                              throws IOException

Create a new process.

Parameters:

runId - run id for logging

enableLogging - enable logging

Returns:

a new SimpleProcess

Throws:

IOException - if an error occurs while creating the process

getToolVersion

public String getToolVersion(RunId runId,
                             String tmpDirPath,
                             List<String> commandLine,
                             boolean parseStdErr,
                             Function<List<String>,String> parser)
                      throws IOException

Get the tool executable version.

Parameters:

runId - the run Id

parseStdErr - parse stderr instead of stdout

Returns:

a string with the tool version

Throws:

IOException - if an error occurs while getting tool version