public class AddMetadataToTaxaTables extends TaxaCountModule implements ApiModule
Modifier and Type | Field and Description |
---|---|
static String |
HIT_RATIO
Metadata column name for column that stores the calculation for:
ParserModuleImpl.getOtuCountField() /
RegisterNumReads.getNumReadFieldName() : "Hit_Ratio". |
static String |
META_MERGED
File suffix added to OTU table file name once merged with metadata.
|
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 |
---|
AddMetadataToTaxaTables() |
Modifier and Type | Method and Description |
---|---|
protected void |
addHitRatioToMetadata()
Add Num_Hits/Num_Reads as Hit_Ratio column to the metadata file
|
void |
cleanUp()
For R to report taxa levels (not HumanN2 reports)
|
protected void |
generateMergedTables()
Create the merged metadata tables.
|
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.
|
protected String |
getMergedLine(String line)
Return OTU table line with metadata row appended (both have PK = sample ID)
|
String |
getSummary()
Produce summary message with min, max, mean, and median hit ratios
|
void |
runModule()
This method matches records from the OTU table and the metadata file by matching the sample ID value in the very
1st column.
|
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, 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, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
checkDependencies, 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 static final String HIT_RATIO
ParserModuleImpl.getOtuCountField()
/
RegisterNumReads.getNumReadFieldName()
: "Hit_Ratio".public static final String META_MERGED
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 addHitRatioToMetadata() throws Exception
Exception
- if unable to build the new metadata columnprotected void generateMergedTables() throws Exception
Exception
- if unable to build tablesprotected String getMergedLine(String line) throws Exception
line
- OTU table lineException
- if unable to create merged linepublic 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