module.report.taxa - RCChan5/BioLockJ GitHub Wiki

Modules in the biolockj.module.report.taxa package process ParserModule output to produce or process taxa tables.

AddMetadataToTaxaTables

#BioModule biolockj.module.report.taxa.AddMetadataToTaxaTables

Description: Map metadata onto taxa tables using sample ID.

metadata.columnDelim
metadata.commentChar
metadata.filePath
metadata.nullValue
report.taxonomyLevels

BuildTaxaTables

#BioModule biolockj.module.report.taxa.BuildTaxaTables

Description: Process ParserModule output to produce taxa tables. This module reads the most recent OTU count files generated by any previous BioModule and re-writes the data as separate tables containing taxa counts for each taxonomy level.

Options:

report.taxonomyLevels

LogTransformTaxaTables

#BioModule biolockj.module.report.taxa.LogTransformTaxaTables

Description: Log-transform the raw taxa counts on Log10 or Log-e scales.

Options:

report.logBase

NormalizeTaxaTables

#BioModule biolockj.module.report.taxa.NormalizeTaxaTables

Description: Normalize taxa tables

Options:

report.logBase