public class QiimeOpenRefClassifier extends QiimeClassifier implements ApiModule
Modifier and Type | Field and Description |
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static String |
PICK_OTU_SCRIPT
Open reference OTU picking script: "pick_open_reference_otus.py"
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ALPHA_DIV_NULL_VALUE, ALPHA_DIVERSITY_TABLE, CITE_QIIME, COMBINED_FNA, EXE_VSEARCH, EXE_VSEARCH_PARAMS, OTU_SUMMARY_FILE, OTU_TABLE, QIIME_PARAMS, QIIME_PYNAST_ALIGN_DB, QIIME_REF_SEQ_DB, QIIME_REMOVE_CHIMERAS, QIIME_TAXA_DB, REP_SET, SCRIPT_ADD_ALPHA_DIVERSITY, SCRIPT_ADD_LABELS, SCRIPT_CALC_ALPHA_DIVERSITY, SCRIPT_FILTER_OTUS, SCRIPT_PRINT_CONFIG, SCRIPT_SUMMARIZE_BIOM, SCRIPT_SUMMARIZE_TAXA, SUMMARIZE_TAXA_SUPPRESS_BIOM
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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QiimeOpenRefClassifier() |
Modifier and Type | Method and Description |
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List<List<String>> |
buildScript(List<File> files)
Return bash script lines to pick open reference OTUs by passing the newest biom file in the temp directory [via
bash code "$(ls -t $tempDir/*.biom | head -1)"] to
QiimeClassifier
getPickOtuLines() method. |
void |
checkDependencies()
Call
QiimeClassifier checkOtuPickingDependencies() method to verify OTU
picking script parameters. |
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()
A extension of
getDescription . |
buildQiimeDockerConfigLines, cleanUp, getClassifierExe, getClassifierParams, getDB, getDockerImageName, getDockerImageOwner, getDockerImageTag, getInputFileDir, getInputFiles, getParams, getPickOtuLines, getPostRequisiteModules, getPreRequisiteModules, getSummary, getVsearchParams, getWorkerScriptFunctions, isValidInputModule
getClassifierType, getDbCache, setDbCache, validateModuleOrder
getSeqFiles
buildScriptForPairedReads, executeTask, 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, 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
cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
getSeqFiles
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
public static final String PICK_OTU_SCRIPT
public List<List<String>> buildScript(List<File> files) throws Exception
QiimeClassifier
getPickOtuLines() method.
Several biom files are generated by this script, the script will select biomFile =
If property "qiime.removeChimeras" =
"Y", use vsearch to identify chimeras and call
"filter_otus_from_otu_table.py" to remove them from
"otu_table.biom"
buildScript
in interface ScriptModule
buildScript
in class QiimeClassifier
files
- Files in the input directory that contain only forward readsException
- if unable to generate script linespublic void checkDependencies() throws Exception
QiimeClassifier
checkOtuPickingDependencies() method to verify OTU
picking script parameters. If not in Docker mode and property
"qiime.removeChimeras" = "Y",
verify "qiime.vsearchParams".checkDependencies
in interface BioModule
checkDependencies
in class QiimeClassifier
Exception
- thrown if missing or invalid dependencies are foundpublic 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