Prepare merged structure organism pairs libraries — prepare_libraries_sop

This function prepares the libraries made of all sub-libraries containing structure-organism pairs

Usage

prepare_libraries_sop_merged(
  files = get_params(step = "prepare_libraries_sop_merged")$files$libraries$sop$prepared,
  filter = get_params(step = "prepare_libraries_sop_merged")$organisms$filter$mode,
  level = get_params(step = "prepare_libraries_sop_merged")$organisms$filter$level,
  value = get_params(step = "prepare_libraries_sop_merged")$organisms$filter$value,
  output_key = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$keys,
  output_org_tax_ott = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$organisms$taxonomies$ott,
  output_str_stereo = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$stereo,
  output_str_met = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$metadata,
  output_str_nam = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$names,
  output_str_tax_cla = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$taxonomies$cla,
  output_str_tax_npc = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$taxonomies$npc
)

Arguments

files: List of libraries to be merged
filter: Boolean. TRUE or FALSE if you want to filter the library
level: Biological rank to be filtered. Kingdom, phylum, family, genus, ...
value: Name of the taxon or taxa to be kept, e.g. 'Gentianaceae|Apocynaceae'
output_key: Output file for keys
output_org_tax_ott: Output file for organisms taxonomy (OTT)
output_str_stereo: Output file for structures stereo
output_str_met: Output file for structures metadata
output_str_nam: Output file for structures names
output_str_tax_cla: Output file for structures taxonomy (Classyfire)
output_str_tax_npc: Output file for structures taxonomy (NPC)

Details

It can be restricted to specific taxa to have more biologically meaningful annotation.

Examples

NULL
#> NULL