public class R_PlotEffectSize extends R_Module implements ApiModule
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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R_PlotEffectSize() |
Modifier and Type | Method and Description |
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void |
checkDependencies()
At least one of the available plot types should NOT be disabled.
|
String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
|
String |
getDescription()
Briefly describe what this module does.
|
protected String |
getModulePrefix()
Returns that prefix to use for property names.
|
protected String |
getModuleRScriptName() |
List<String> |
getPreRequisiteModules()
Returns
Constants.DEFAULT_STATS_MODULE and if fold change plots are to be generated, add
NormalizeTaxaTables |
buildScript, calcTimeout, cleanUp, executeTask, getCustomScriptProp, getDockerImageName, getDockerImageOwner, getDockerImageTag, getFunctionLib, getFunctionLib, getModuleRScript, getTimeout, grapRUsedProps, requiredRPackages
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getWorkerScriptFunctions, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
public void checkDependencies() throws Exception
checkDependencies
in interface BioModule
checkDependencies
in class R_Module
Exception
- thrown if missing or invalid dependencies are foundpublic List<String> getPreRequisiteModules() throws Exception
Constants.DEFAULT_STATS_MODULE
and if fold change plots are to be generated, add
NormalizeTaxaTables
getPreRequisiteModules
in interface BioModule
getPreRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as prerequisitespublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule
protected String getModuleRScriptName()
getModuleRScriptName
in class R_Module
protected String getModulePrefix()
R_Module
getModulePrefix
in class R_Module