public class R_PlotMds extends R_Module implements ApiModule
Modifier and Type | Field and Description |
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protected static String |
R_MDS_DISTANCE
Config property: "r_PlotMds.distance" defines the distance index to use in the capscale
command. |
protected static String |
R_MDS_NUM_AXIS
Config Integer property: "r_PlotMds.numAxis" defines the number of MDS axis to report |
protected static String |
R_MDS_REPORT_FIELDS
Config List property: "r_PlotMds.reportFields"List metadata fields to generate MDS ordination plots. |
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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R_PlotMds() |
Modifier and Type | Method and Description |
---|---|
void |
checkDependencies()
Require
Config ."r_PlotMds.numAxis" set to integer greater than 2 |
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 |
getModulePrefix()
Returns that prefix to use for property names.
|
protected String |
getModuleRScriptName() |
protected Map<String,String> |
requiredRPackages() |
String |
version()
Changes to a module class should be accompanied by a increment in version.
|
buildScript, calcTimeout, cleanUp, executeTask, getCustomScriptProp, getDockerImageName, getDockerImageOwner, getDockerImageTag, getFunctionLib, getFunctionLib, getModuleRScript, getTimeout, grapRUsedProps
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getWorkerScriptFunctions, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias
protected static final String R_MDS_DISTANCE
Config
property: "r_PlotMds.distance" defines the distance index to use in the capscale
command.protected static final String R_MDS_NUM_AXIS
Config
Integer property: "r_PlotMds.numAxis" defines the number of MDS axis to reportprotected static final String R_MDS_REPORT_FIELDS
Config
List property: "r_PlotMds.reportFields"public void checkDependencies() throws Exception
Config
."r_PlotMds.numAxis" set to integer greater than 2checkDependencies
in interface BioModule
checkDependencies
in class R_Module
Exception
- thrown if missing or invalid dependencies are foundprotected Map<String,String> requiredRPackages()
requiredRPackages
in class R_Module
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule
public String version()
BioModule
protected String getModuleRScriptName()
getModuleRScriptName
in class R_Module
protected String getModulePrefix()
R_Module
getModulePrefix
in class R_Module