public class BuildTaxaTables extends OtuCountModule 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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BuildTaxaTables() |
Modifier and Type | Method and Description |
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protected void |
buildTaxonomyTables(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts)
Build taxonomy tables from the sampleTaxaCounts.
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String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
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String |
getDescription()
Briefly describe what this module does.
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String |
getDetails()
A extension of
getDescription . |
String |
getSummary()
Returns summary message to be displayed by Email module so must not contain confidential info.
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void |
runModule()
This method executes the modules primary Java routine.
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getInputFiles, isOtuModule, 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, getPreRequisiteModules, 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, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
public String getSummary() throws Exception
ScriptModuleImpl
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic void runModule() throws Exception
JavaModule
runModule
in interface JavaModule
runModule
in class JavaModuleImpl
Exception
- thrown if any runtime error occursprotected void buildTaxonomyTables(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts) throws Exception
sampleOtuCounts
- TreeMap(SampleId, TreeMap(OTU, count)) OTU counts for every sampleException
- if errors occurpublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getDetails()
ApiModule
getDescription
. Beyond the brief description, give details such as
the interaction between properties.getDetails
in interface ApiModule
getDetails
in class BioModuleImpl
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule