biolockj.module.implicit.qiime

Class MergeQiimeOtuTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.implicit.qiime.MergeQiimeOtuTables

All Implemented Interfaces:

BioModule, ScriptModule, Comparable<BioModule>

public class MergeQiimeOtuTables
extends ScriptModuleImpl

This BioModule will run immediately after QiimeClosedRefClassifier if multiple otu_table.biom files were created.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	SCRIPT_MERGE_OTU_TABLES QIIME script to merge multiple OTU tables in biom format.

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
MergeQiimeOtuTables()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Build a single bash script line to call "merge_otu_tables.py" to create the single "otu_table.biom", as required by QiimeParser.
void	checkDependencies() Verify the previous module = QiimeClosedRefClassifier
void	executeTask() Call buildScript(List) to create bash script lines needed to merge "otu_table.biom"s with "merge_otu_tables.py" unless only 1 input file found, in which case, just copy it to the output dir.
String	getDockerImageName() Get the docker image to use for this module.
String	getDockerImageOwner() Get the name of the docker hub user that owns the image to use for this module.
String	getDockerImageTag() Get the version / tag to use for the docker image.
boolean	isValidInputModule(BioModule module) In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input.

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.BioModule

cleanUp, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version

Field Detail

SCRIPT_MERGE_OTU_TABLES

protected static final String SCRIPT_MERGE_OTU_TABLES

QIIME script to merge multiple OTU tables in biom format.

See Also:

Constant Field Values

Constructor Detail

MergeQiimeOtuTables

public MergeQiimeOtuTables()

Method Detail

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Build a single bash script line to call "merge_otu_tables.py" to create the single "otu_table.biom", as required by QiimeParser.

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

checkDependencies

public void checkDependencies()
                       throws Exception

Verify the previous module = QiimeClosedRefClassifier

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

executeTask

public void executeTask()
                 throws Exception

Call buildScript(List) to create bash script lines needed to merge "otu_table.biom"s with "merge_otu_tables.py" unless only 1 input file found, in which case, just copy it to the output dir.

Specified by:

executeTask in interface BioModule

Overrides:

executeTask in class ScriptModuleImpl

Throws:

Exception - thrown if the module is unable to complete is task

isValidInputModule

public boolean isValidInputModule(BioModule module)

Description copied from class: BioModuleImpl

In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input. This method returns false if the previousModule only produced a new metadata file, such as ImportMetadata or RegisterNumReads. When BioModuleImpl.getInputFiles() is called, this method determines if the previousModule output is valid input for the current BioModule. The default implementation of this method returns FALSE if the previousModule only generates a new metadata file.

Specified by:

isValidInputModule in interface BioModule

Overrides:

isValidInputModule in class BioModuleImpl

Parameters:

module - BioModule that ran before the current BioModule

Returns:

boolean TRUE if the previousModule output is acceptable input for the current BioModule

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Returns:

getDockerImageTag

public String getDockerImageTag()

Description copied from interface: BioModule

Get the version / tag to use for the docker image. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageTag in interface BioModule

Overrides:

getDockerImageTag in class BioModuleImpl

Returns: