public class AddPseudoCount extends TransformTaxaTables implements ApiModule
BLJ_OPTIONS
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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AddPseudoCount() |
Modifier and Type | Method and Description |
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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.
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protected String |
getProcessSuffix() |
String |
getSummary()
Returns summary message to be displayed by Email module so must not contain confidential info.
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protected TaxaLevelTable |
transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Transform a table of values.
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filterSamples, filterTaxa, getOutputFile, runModule
filterByProcessLevel, getDetails, getInputFiles, getPreRequisiteModules, isTaxaModule, isValidInputModule
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
protected TaxaLevelTable transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) throws Exception
TransformTaxaTables
transform
in class TransformTaxaTables
inputData
- the data to be transformed without filteringfilteredSampleIDs
- Sample ids after filteringfilteredTaxaIDs
- Taxa names after filteringException
public String getSummary() throws Exception
ScriptModuleImpl
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occursprotected String getProcessSuffix()
getProcessSuffix
in class TransformTaxaTables
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule