public class NormalizeByReadsPerMillion 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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NormalizeByReadsPerMillion() |
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.
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List<String> |
getPreRequisiteModules()
Require taxonomy table module as prerequisite
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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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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, 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, 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
TransformTaxaTables
transform
in class TransformTaxaTables
inputData
- the data to be transformed without filteringfilteredSampleIDs
- Sample ids after filteringfilteredTaxaIDs
- Taxa names after filteringException
protected String getProcessSuffix()
getProcessSuffix
in class TransformTaxaTables
public String getSummary() throws Exception
ScriptModuleImpl
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic List<String> getPostRequisiteModules() throws Exception
BioModuleImpl
getPostRequisiteModules
in interface BioModule
getPostRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as post-requisitespublic List<String> getPreRequisiteModules() throws Exception
TaxaCountModule
getPreRequisiteModules
in interface BioModule
getPreRequisiteModules
in class TaxaCountModule
Exception
- if invalid Class names are returned as prerequisitespublic 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