public class ShannonDiversity extends TransformTaxaTables implements ApiModule
Modifier and Type | Field and Description |
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static String |
SHANNON_COLUMN |
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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ShannonDiversity() |
Modifier and Type | Method and Description |
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protected List<String> |
filterTaxa(TaxaLevelTable inputData) |
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 |
getProcessSuffix() |
boolean |
isValidInputModule(BioModule module)
If module is a
SeqModule input must contain sequence data. |
protected TaxaLevelTable |
transform(TaxaLevelTable inputData,
List<String> filteredSampleIDs,
List<String> filteredTaxaIDs)
Transform a table of values.
|
String |
version()
Changes to a module class should be accompanied by a increment in version.
|
filterSamples, getOutputFile, runModule
filterByProcessLevel, getDetails, getInputFiles, getPreRequisiteModules, isTaxaModule
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, 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, getSummary, getTempDir, init, setAlias
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
public static final String SHANNON_COLUMN
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 List<String> filterTaxa(TaxaLevelTable inputData)
filterTaxa
in class TransformTaxaTables
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule
public String version()
BioModule
public boolean isValidInputModule(BioModule module)
JavaModuleImpl
SeqModule
input must contain sequence data.isValidInputModule
in interface BioModule
isValidInputModule
in class TaxaCountModule
module
- BioModule that ran before the current BioModuleprotected String getProcessSuffix()
getProcessSuffix
in class TransformTaxaTables