public class NormalizeTaxaTables extends TransformTaxaTables implements ApiModule
Constants.REPORT_LOG_BASE
property.
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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NormalizeTaxaTables() |
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.
|
String |
getDetails()
All child classes from this class have this pre-req.
|
List<String> |
getPostRequisiteModules()
By default, no post-requisites are required.
|
protected String |
getProcessSuffix() |
String |
getSummary()
Returns summary message to be displayed by Email module so must not contain confidential info.
|
protected TaxaLevelTable |
transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1
|
String |
version()
Changes to a module class should be accompanied by a increment in version.
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filterSamples, filterTaxa, getOutputFile, runModule
filterByProcessLevel, 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, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
protected TaxaLevelTable transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) throws Exception
transform
in class TransformTaxaTables
taxaTable
- OTU raw count tableException
- if unable to construct NormalizeTaxaTablespublic 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 List<String> getPostRequisiteModules() throws Exception
BioModuleImpl
getPostRequisiteModules
in interface BioModule
getPostRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as post-requisitespublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getDetails() throws API_Exception
TaxaCountModule
getDetails
in interface ApiModule
getDetails
in class TaxaCountModule
API_Exception
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule