public class AddMetadataToPathwayTables extends Humann2CountModule
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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AddMetadataToPathwayTables() |
Modifier and Type | Method and Description |
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void |
cleanUp()
For R to report HumanN2 reports instead of taxa levels
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protected void |
generateMergedTables()
Create the merged metadata tables.
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protected String |
getMergedLine(String line)
Return OTU table line with metadata row appended (both have PK = sample ID)
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String |
getSummary()
Produce summary message with min, max, mean, and median hit ratios
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void |
runModule()
This method matches records from the Pathway Abundance table and the metadata file by matching the sample ID
value in the very 1st column (regardless of column title).
Set |
checkDependencies, getInputFiles, getPreRequisiteModules, isHumann2CountModule, isValidInputModule
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, 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
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version
public void cleanUp() throws Exception
cleanUp
in interface BioModule
cleanUp
in class BioModuleImpl
Exception
- thrown if any runtime error occurspublic String getSummary() throws Exception
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic void runModule() throws Exception
runModule
in interface JavaModule
runModule
in class JavaModuleImpl
Exception
- thrown if any runtime error occursprotected void generateMergedTables() throws Exception
Exception
- if unable to build tables