public class MergeQiimeOtuTables extends ScriptModuleImpl
Modifier and Type | Field and Description |
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protected static String |
SCRIPT_MERGE_OTU_TABLES
QIIME script to merge multiple OTU tables in biom format.
|
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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MergeQiimeOtuTables() |
Modifier and Type | Method and Description |
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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.
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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. |
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, hasScripts, isValidProp
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
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
cleanUp, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version
protected static final String SCRIPT_MERGE_OTU_TABLES
public List<List<String>> buildScript(List<File> files) throws Exception
QiimeParser
.buildScript
in interface ScriptModule
buildScript
in class ScriptModuleImpl
files
- Files in the input directory that contain only forward readsException
- if unable to generate script linespublic void checkDependencies() throws Exception
QiimeClosedRefClassifier
checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic void executeTask() throws Exception
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.executeTask
in interface BioModule
executeTask
in class ScriptModuleImpl
Exception
- thrown if the module is unable to complete is taskpublic boolean isValidInputModule(BioModule module)
BioModuleImpl
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.isValidInputModule
in interface BioModule
isValidInputModule
in class BioModuleImpl
module
- BioModule that ran before the current BioModulepublic String getDockerImageOwner()
BioModule
getDockerImageOwner
in interface BioModule
getDockerImageOwner
in class BioModuleImpl
public String getDockerImageName()
BioModule
public String getDockerImageTag()
BioModule
getDockerImageTag
in interface BioModule
getDockerImageTag
in class BioModuleImpl