QiimeClassifier

java.lang.Object
- biolockj.module.BioModuleImpl
- - biolockj.module.ScriptModuleImpl
  - - biolockj.module.SeqModuleImpl
    - - biolockj.module.classifier.ClassifierModuleImpl
      - biolockj.module.implicit.qiime.QiimeClassifier

All Implemented Interfaces:

BioModule, ClassifierModule, DatabaseModule, ScriptModule, SeqModule, Comparable<BioModule>

Direct Known Subclasses:

QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier
```
public class QiimeClassifier
extends ClassifierModuleImpl
```
This BioModule generates the bash script used to create QIIME summary scripts, taxonomy-level reports, and add alpha diversity metrics (if configured) to the metadata file.
For a complete list of available metrics, see: http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html

GUI Module Name

Field Summary

Fields
Modifier and Type	Field and Description
`protected static String`	`ALPHA_DIV_NULL_VALUE` Value output by "alpha_diversity.py" for null values: "N/A"
`protected static String`	`ALPHA_DIVERSITY_TABLE` File produced by QIIME "alpha_diversity.py" script: "alphaDiversity.txt"
`protected static String`	`COMBINED_FNA` Multiplexed fasta file produced by QIIME "add_qiime_labels.py" script: "combined_seqs.fna"
`protected static String`	`EXE_VSEARCH` `Config` property for vsearch exectuable used for chimera detection: "exe.vsearch"
`protected static String`	`EXE_VSEARCH_PARAMS` `Config` property for "exe.vsearch" parameters (such as alternate reference database path): "exe.vsearchParams"
`protected static String`	`OTU_SUMMARY_FILE` File produced by QIIME "biom summarize-table" script: "otuSummary.txt"
`protected static String`	`OTU_TABLE` File produced by OTU picking scripts holding read taxonomy assignments: "otu_table.biom"
`protected static String`	`QIIME_PARAMS` `Config` List property used to obtain the QIIME executable params
`protected static String`	`QIIME_PYNAST_ALIGN_DB` `Config` File property to define ~/.qiime_config pynast_template_alignment_fp: "qiime.pynastAlignDB"
`protected static String`	`QIIME_REF_SEQ_DB` `Config` File property to define ~/.qiime_config pick_otus_reference_seqs_fp and assign_taxonomy_reference_seqs_fp: "qiime.refSeqDB"
`protected static String`	`QIIME_REMOVE_CHIMERAS` `Config` boolean property to indicate if "exe.vsearch" is needed for chimera removal: "qiime.removeChimeras"
`protected static String`	`QIIME_TAXA_DB` `Config` File property to define ~/.qiime_config assign_taxonomy_id_to_taxonomy_fp: "qiime.taxaDB"
`protected static String`	`REP_SET` Directory created by "pick_de_novo_otus.py" and "pick_open_reference_otus.py": "rep_set"
`protected static String`	`SCRIPT_ADD_ALPHA_DIVERSITY` QIIME script to add "alphaDiversity.txt" to the metadata file: "add_alpha_to_mapping_file.py"
`protected static String`	`SCRIPT_ADD_LABELS` QIIME script that produces "combined_seqs.fna", the multiplexed fasta file: "add_qiime_labels.py"
`protected static String`	`SCRIPT_CALC_ALPHA_DIVERSITY` QIIME script that creates alpha diversity metrics file in output/"alphaDiversity.txt": "alpha_diversity.py"
`protected static String`	`SCRIPT_FILTER_OTUS` QIIME script used to remove chimeras detected by "exe.vsearch": "filter_otus_from_otu_table.py"
`protected static String`	`SCRIPT_PRINT_CONFIG` QIIME script to print environment configuration to qsub output file: "print_qiime_config.py"
`protected static String`	`SCRIPT_SUMMARIZE_BIOM` Produces output/"otuSummary.txt" summarizing dataset: "biom summarize-table"
`protected static String`	`SCRIPT_SUMMARIZE_TAXA` QIIME script used to produce taxonomy-level reports in the module output directory: "summarize_taxa.py"
`protected static String`	`SUMMARIZE_TAXA_SUPPRESS_BIOM` QIIME script "summarize_taxa.py" parameter used to suppress the output of biom files.

Fields inherited from class biolockj.module.BioModuleImpl
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.ScriptModule
SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule
MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors
Constructor and Description

QiimeClassifier()

Constructors
Constructor and Description
`QiimeClassifier()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected List<String>`	`buildQiimeDockerConfigLines()` Build ~/.qiime_config to define the alternate Docker qiime_classifier DB with local container path references.
`List<List<String>>`	`buildScript(List<File> files)` Generate bash script lines to summarize QIIME results, build taxonomy reports, and add alpha diversity metrics.
`List<List<String>>`	`buildScriptForPairedReads(List<File> files)` QIIME does not support paired reads
`void`	`checkDependencies()` Validate module dependencies: Call `ClassifierModuleImpl.getClassifierExe()` to verify the executable Call `ClassifierModuleImpl.getClassifierParams()` to verify the runtime parameters are valid Call `ClassifierModuleImpl.validateModuleOrder()` to validate module configuration order.
`void`	`cleanUp()` The cleanUp operation builds a new metadata file if alpha diversity metrics were generated by this module.
`String`	`getClassifierExe()` QIIME calls python scripts, so no special command is required
`List<String>`	`getClassifierParams()` Obtain the QIIME runtime params
`File`	`getDB()` Check DB parameters for the comment parent directory path, there are 3 parameters: "qiime.pynastAlignDB" "qiime.refSeqDB" "qiime.taxaDB"
`protected File`	`getDockerDB(String prop)` Return the Docker container database directory (starting with /db/...)
`protected File`	`getInputFileDir()` Module input directories are set to the previous module output directory. To ensure we use the correct path, get path from `getInputFiles()`
`List<File>`	`getInputFiles()` Return `SeqModuleImpl.getSeqFiles(Collection)` to filter standard module input files.
`protected String`	`getParams()` Subclasses call this method to check dependencies before picking OTUs to validate `Config`."qiime.params"
`protected List<String>`	`getPickOtuLines(String otuPickingScript, File fastaDir, String mapping, File outputDir)` Subclasses call this method to add OTU picking lines by calling "add_qiime_labels.py" via OTU picking script.
`List<String>`	`getPostRequisiteModules()` Subclasses of QiimeClassifier add post-requisite module: `QiimeClassifier`.
`List<String>`	`getPreRequisiteModules()` If paired reads found, add prerequisite module: `PearMergeReads`.
`String`	`getSummary()` This method extends the classifier summary by adding the Qiime OTU summary metrics.
`protected String`	`getVsearchParams()` Return runtime parameters for "exe.vsearchParams"
`List<String>`	`getWorkerScriptFunctions()` Method returns bash script lines used to build the functions called by the worker scripts.
`boolean`	`isValidInputModule(BioModule module)` If superclass is fed by another QiimeClassifier, it must be a subclass with biom output.
`protected void`	`validateFileNameUnique(Set<String> fileNames, File file)` Typically we verify no duplicate file names are used, but for QIIME we may be combining multiple files with the same name ("otu_table.biom"), so QiimeClassifier skips this validation.

Methods inherited from class biolockj.module.classifier.ClassifierModuleImpl
getClassifierType, validateModuleOrder

Methods inherited from class biolockj.module.SeqModuleImpl
getSeqFiles

Methods inherited from class biolockj.module.ScriptModuleImpl
executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl
cacheInputFiles, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, getTempDir, init, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.SeqModule
getSeqFiles

Methods inherited from interface biolockj.module.ScriptModule
getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule
executeTask, getID, getModuleDir, getOutputDir, getTempDir, init

- Field Detail
  - ALPHA_DIV_NULL_VALUE
```
protected static final String ALPHA_DIV_NULL_VALUE
```
    Value output by "alpha_diversity.py" for null values: "N/A"
    
    See Also:
    
    Constant Field Values
  - ALPHA_DIVERSITY_TABLE
```
protected static final String ALPHA_DIVERSITY_TABLE
```
    File produced by QIIME "alpha_diversity.py" script: "alphaDiversity.txt"
    
    See Also:
    
    Constant Field Values
  - COMBINED_FNA
```
protected static final String COMBINED_FNA
```
    Multiplexed fasta file produced by QIIME "add_qiime_labels.py" script: "combined_seqs.fna"
    
    See Also:
    
    Constant Field Values
  - EXE_VSEARCH
```
protected static final String EXE_VSEARCH
```
    Config property for vsearch exectuable used for chimera detection: "exe.vsearch"
    
    See Also:
    
    Constant Field Values
  - EXE_VSEARCH_PARAMS
```
protected static final String EXE_VSEARCH_PARAMS
```
    Config property for "exe.vsearch" parameters (such as alternate reference database path): "exe.vsearchParams"
    
    See Also:
    
    Constant Field Values
  - OTU_SUMMARY_FILE
```
protected static final String OTU_SUMMARY_FILE
```
    File produced by QIIME "biom summarize-table" script: "otuSummary.txt"
    
    See Also:
    
    Constant Field Values
  - OTU_TABLE
```
protected static final String OTU_TABLE
```
    File produced by OTU picking scripts holding read taxonomy assignments: "otu_table.biom"
    
    See Also:
    
    Constant Field Values
  - QIIME_PARAMS
```
protected static final String QIIME_PARAMS
```
    Config List property used to obtain the QIIME executable params
    
    See Also:
    
    Constant Field Values
  - QIIME_PYNAST_ALIGN_DB
```
protected static final String QIIME_PYNAST_ALIGN_DB
```
    Config File property to define ~/.qiime_config pynast_template_alignment_fp: "qiime.pynastAlignDB"
    
    See Also:
    
    Constant Field Values
  - QIIME_REF_SEQ_DB
```
protected static final String QIIME_REF_SEQ_DB
```
    Config File property to define ~/.qiime_config pick_otus_reference_seqs_fp and assign_taxonomy_reference_seqs_fp: "qiime.refSeqDB"
    
    See Also:
    
    Constant Field Values
  - QIIME_REMOVE_CHIMERAS
```
protected static final String QIIME_REMOVE_CHIMERAS
```
    Config boolean property to indicate if "exe.vsearch" is needed for chimera removal: "qiime.removeChimeras"
    
    See Also:
    
    Constant Field Values
  - QIIME_TAXA_DB
```
protected static final String QIIME_TAXA_DB
```
    Config File property to define ~/.qiime_config assign_taxonomy_id_to_taxonomy_fp: "qiime.taxaDB"
    
    See Also:
    
    Constant Field Values
  - REP_SET
```
protected static final String REP_SET
```
    Directory created by "pick_de_novo_otus.py" and "pick_open_reference_otus.py": "rep_set"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_ADD_ALPHA_DIVERSITY
```
protected static final String SCRIPT_ADD_ALPHA_DIVERSITY
```
    QIIME script to add "alphaDiversity.txt" to the metadata file: "add_alpha_to_mapping_file.py"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_ADD_LABELS
```
protected static final String SCRIPT_ADD_LABELS
```
    QIIME script that produces "combined_seqs.fna", the multiplexed fasta file: "add_qiime_labels.py"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_CALC_ALPHA_DIVERSITY
```
protected static final String SCRIPT_CALC_ALPHA_DIVERSITY
```
    QIIME script that creates alpha diversity metrics file in output/"alphaDiversity.txt": "alpha_diversity.py"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_FILTER_OTUS
```
protected static final String SCRIPT_FILTER_OTUS
```
    QIIME script used to remove chimeras detected by "exe.vsearch": "filter_otus_from_otu_table.py"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_PRINT_CONFIG
```
protected static final String SCRIPT_PRINT_CONFIG
```
    QIIME script to print environment configuration to qsub output file: "print_qiime_config.py"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_SUMMARIZE_BIOM
```
protected static final String SCRIPT_SUMMARIZE_BIOM
```
    Produces output/"otuSummary.txt" summarizing dataset: "biom summarize-table"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_SUMMARIZE_TAXA
```
protected static final String SCRIPT_SUMMARIZE_TAXA
```
    QIIME script used to produce taxonomy-level reports in the module output directory: "summarize_taxa.py"
    
    See Also:
    
    Constant Field Values
  - SUMMARIZE_TAXA_SUPPRESS_BIOM
```
protected static final String SUMMARIZE_TAXA_SUPPRESS_BIOM
```
    QIIME script "summarize_taxa.py" parameter used to suppress the output of biom files. BioLockJ BioLockJ parsers expect clear text files in the module output directory, so the biom files must be excluded.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - QiimeClassifier
```
public QiimeClassifier()
```
- Method Detail
  - buildScript
```
public List<List<String>> buildScript(List<File> files)
                               throws Exception
```
    Generate bash script lines to summarize QIIME results, build taxonomy reports, and add alpha diversity metrics.
    The QiimeClassifier script begins with the following QIIME scripts:
    1. "print_qiime_config.py" - logs version/environment info
    2. "summarize_taxa.py" - processes "otu_table.biom" to create taxonomy-level reports in the output directory
    3. "biom summarize-table" - processes "otu_table.biom" to create summary file: output/"otuSummary.txt"
    If Config. are defined, add lines to run additional scripts:
    1. "alpha_diversity.py" - calculates on "otu_table.biom" to create output/"alphaDiversity.txt"
    2. "add_alpha_to_mapping_file.py" - adds "alphaDiversity.txt" data to Config."metadata.filePath"
    For complete list of skbio.diversity.alpha options, see http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html
    Specified by:
    
    buildScript in interface ScriptModule
    
    Specified by:
    
    buildScript in class ScriptModuleImpl
    
    Parameters:
    
    files - Files in the input directory that contain only forward reads
    
    Returns:
    
    Nested list of bash scripts lines
    
    Throws:
    
    Exception - if unable to generate script lines
  - buildScriptForPairedReads
```
public List<List<String>> buildScriptForPairedReads(List<File> files)
                                             throws Exception
```
    QIIME does not support paired reads
    
    Specified by:
    
    buildScriptForPairedReads in interface ScriptModule
    
    Overrides:
    
    buildScriptForPairedReads in class ScriptModuleImpl
    
    Parameters:
    
    files - Files in the input directory that contain only paired reads
    
    Returns:
    
    Nested list of bash scripts lines
    
    Throws:
    
    Exception - if unable to generate the script lines
  - checkDependencies
```
public void checkDependencies()
                       throws Exception
```
    Description copied from class: ClassifierModuleImpl
    Validate module dependencies:
    - Call ClassifierModuleImpl.getClassifierExe() to verify the executable
    - Call ClassifierModuleImpl.getClassifierParams() to verify the runtime parameters are valid
    - Call ClassifierModuleImpl.validateModuleOrder() to validate module configuration order.
    - Call BioModule.checkDependencies() to validate script dependencies.
    Specified by:
    
    checkDependencies in interface BioModule
    
    Overrides:
    
    checkDependencies in class ClassifierModuleImpl
    
    Throws:
    
    Exception - thrown if missing or invalid dependencies are found
  - cleanUp
```
public void cleanUp()
             throws Exception
```
    The cleanUp operation builds a new metadata file if alpha diversity metrics were generated by this module. The script "add_alpha_to_mapping_file.py" outputs "N/A" for null values which must be replaced by Config."metadata.nullValue" if any are found.
    This method also removes the redundant normalized alpha metric column and reorganizes the metadata so that alpha metric columns are move to the first columns after the 1st ID column.
    
    Specified by:
    
    cleanUp in interface BioModule
    
    Overrides:
    
    cleanUp in class BioModuleImpl
    
    Throws:
    
    Exception - thrown if any runtime error occurs
  - getClassifierExe
```
public String getClassifierExe()
                        throws Exception
```
    QIIME calls python scripts, so no special command is required
    
    Specified by:
    
    getClassifierExe in interface ClassifierModule
    
    Specified by:
    
    getClassifierExe in class ClassifierModuleImpl
    
    Returns:
    
    Command to execute classifier program
    
    Throws:
    
    Exception - if the classifier program undefined or invalid
  - getClassifierParams
```
public List<String> getClassifierParams()
                                 throws Exception
```
    Obtain the QIIME runtime params
    
    Specified by:
    
    getClassifierParams in interface ClassifierModule
    
    Specified by:
    
    getClassifierParams in class ClassifierModuleImpl
    
    Returns:
    
    Runtime parameters
    
    Throws:
    
    Exception - thrown if parameters defined are invalid
  - getDB
```
public File getDB()
           throws Exception
```
    Check DB parameters for the comment parent directory path, there are 3 parameters:
    Specified by:
    
    getDB in interface DatabaseModule
    
    Specified by:
    
    getDB in class ClassifierModuleImpl
    
    Returns:
    
    Parent DB directory
    
    Throws:
    
    Exception - if errors occur
  - getInputFiles
```
public List<File> getInputFiles()
                         throws Exception
```
    Description copied from class: SeqModuleImpl
    
    Return SeqModuleImpl.getSeqFiles(Collection) to filter standard module input files.
    
    Specified by:
    
    getInputFiles in interface BioModule
    
    Overrides:
    
    getInputFiles in class SeqModuleImpl
    
    Returns:
    
    Input files
    
    Throws:
    
    Exception - thrown if any runtime error occurs
  - getPostRequisiteModules
```
public List<String> getPostRequisiteModules()
                                     throws Exception
```
    Subclasses of QiimeClassifier add post-requisite module: QiimeClassifier. Only the QiimeClassifier itself adds the QiimeParser as a post-requisite module.
    
    Specified by:
    
    getPostRequisiteModules in interface BioModule
    
    Overrides:
    
    getPostRequisiteModules in class ClassifierModuleImpl
    
    Returns:
    
    List of BioModules
    
    Throws:
    
    Exception - if invalid Class names are returned as post-requisites
  - getPreRequisiteModules
```
public List<String> getPreRequisiteModules()
                                    throws Exception
```
    If paired reads found, add prerequisite module: PearMergeReads. If sequences are not fasta format, add prerequisite module: AwkFastaConverter, or similar module specified by "pipeline.defaultFastaConverter". Subclasses of QiimeClassifier add prerequisite module: BuildQiimeMapping.
    
    Specified by:
    
    getPreRequisiteModules in interface BioModule
    
    Overrides:
    
    getPreRequisiteModules in class BioModuleImpl
    
    Returns:
    
    List of BioModule Class Names
    
    Throws:
    
    Exception - if invalid Class names are returned as prerequisites
  - getSummary
```
public String getSummary()
                  throws Exception
```
    This method extends the classifier summary by adding the Qiime OTU summary metrics.
    
    Specified by:
    
    getSummary in interface BioModule
    
    Overrides:
    
    getSummary in class ClassifierModuleImpl
    
    Returns:
    
    Summary of BioModule execution
    
    Throws:
    
    Exception - if any error occurs
  - getWorkerScriptFunctions
```
public List<String> getWorkerScriptFunctions()
                                      throws Exception
```
    Description copied from interface: ScriptModule
    
    Method returns bash script lines used to build the functions called by the worker scripts.
    
    Specified by:
    
    getWorkerScriptFunctions in interface ScriptModule
    
    Overrides:
    
    getWorkerScriptFunctions in class ScriptModuleImpl
    
    Returns:
    
    Bash script lines for the functions
    
    Throws:
    
    Exception - if errors occur
  - isValidInputModule
```
public boolean isValidInputModule(BioModule module)
```
    If superclass is fed by another QiimeClassifier, it must be a subclass with biom output. Otherwise, if a subclass, it must expect sequence file input.
    
    Specified by:
    
    isValidInputModule in interface BioModule
    
    Overrides:
    
    isValidInputModule in class SeqModuleImpl
    
    Parameters:
    
    module - BioModule that ran before the current BioModule
    
    Returns:
    
    boolean TRUE if the previousModule output is acceptable input for the current BioModule
  - buildQiimeDockerConfigLines
```
protected List<String> buildQiimeDockerConfigLines()
                                            throws Exception
```
    Build ~/.qiime_config to define the alternate Docker qiime_classifier DB with local container path references.
    
    Returns:
    
    Bash script lines to build the qiime_config file
    
    Throws:
    
    Exception - if errors occur build file
  - getDockerDB
```
protected File getDockerDB(String prop)
                    throws Exception
```
    Return the Docker container database directory (starting with /db/...)
    
    Parameters:
    
    prop - QIIME database dir
    
    Returns:
    
    Docker container DB dir
    
    Throws:
    
    Exception - if errors occur
  - getInputFileDir
```
protected File getInputFileDir()
                        throws Exception
```
    Module input directories are set to the previous module output directory.
    To ensure we use the correct path, get path from getInputFiles()
    
    Returns:
    
    File directory containing module input files
    
    Throws:
    
    Exception - if propagated by getInputFiles()
  - getParams
```
protected String getParams()
                    throws Exception
```
    Subclasses call this method to check dependencies before picking OTUs to validate Config."qiime.params"
    
    Returns:
    
    Validated QIIME runtime parameters
    
    Throws:
    
    Exception - if "qiime.params" contains invalid parameters
  - getPickOtuLines
```
protected List<String> getPickOtuLines(String otuPickingScript,
                                       File fastaDir,
                                       String mapping,
                                       File outputDir)
                                throws Exception
```
    Subclasses call this method to add OTU picking lines by calling "add_qiime_labels.py" via OTU picking script. Sleep for 5 seconds before running so that freshly created batch fasta files and mapping files can be found on the file system.
    
    Parameters:
    
    otuPickingScript - QIIME script
    
    fastaDir - Fasta File directory
    
    mapping - File-path of mapping file
    
    outputDir - Directory to output "combined_seqs.fna"
    
    Returns:
    
    2 script lines for the bash script
    
    Throws:
    
    Exception - if errors occur
  - getVsearchParams
```
protected String getVsearchParams()
                           throws Exception
```
    Return runtime parameters for "exe.vsearchParams"
    
    Returns:
    
    Vsearch runtime parameters
    
    Throws:
    
    Exception - if errors occur
  - validateFileNameUnique
```
protected void validateFileNameUnique(Set<String> fileNames,
                                      File file)
```
    Typically we verify no duplicate file names are used, but for QIIME we may be combining multiple files with the same name ("otu_table.biom"), so QiimeClassifier skips this validation.
    
    Overrides:
    
    validateFileNameUnique in class BioModuleImpl
    
    Parameters:
    
    fileNames - A registry of module input file names added so far
    
    file - Next file to validate

Class QiimeClassifier

Field Summary

Fields inherited from class biolockj.module.BioModuleImpl

Fields inherited from interface biolockj.module.ScriptModule

Fields inherited from interface biolockj.module.BioModule

Constructor Summary

Method Summary

Methods inherited from class biolockj.module.classifier.ClassifierModuleImpl

Methods inherited from class biolockj.module.SeqModuleImpl

Methods inherited from class biolockj.module.ScriptModuleImpl

Methods inherited from class biolockj.module.BioModuleImpl

Methods inherited from class java.lang.Object

Methods inherited from interface biolockj.module.SeqModule

Methods inherited from interface biolockj.module.ScriptModule

Methods inherited from interface biolockj.module.BioModule

Field Detail

ALPHA_DIV_NULL_VALUE

ALPHA_DIVERSITY_TABLE

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

Constructor Detail

QiimeClassifier

Method Detail

buildScript

buildScriptForPairedReads

checkDependencies

cleanUp

getClassifierExe

getClassifierParams

getDB

getInputFiles

getPostRequisiteModules

getPreRequisiteModules

getSummary

getWorkerScriptFunctions

isValidInputModule

buildQiimeDockerConfigLines

getDockerDB

getInputFileDir

getParams

getPickOtuLines

getVsearchParams

validateFileNameUnique