Get default paths

This function gets default paths

Usage

get_default_paths(yaml = system.file("paths.yaml", package = "tima"))

Arguments

yaml

The YAML file containing the paths (default is "paths.yaml")

Value

A list containing the paths specified in the YAML file

Examples

get_default_paths()
#> $base_dir
#> [1] "./"
#> 
#> $data
#> $data$path
#> [1] "data"
#> 
#> $data$interim
#> $data$interim$path
#> [1] "data/interim"
#> 
#> $data$interim$annotations
#> $data$interim$annotations$path
#> [1] "data/interim/annotations"
#> 
#> $data$interim$annotations$example_sirius
#> $data$interim$annotations$example_sirius$v5
#> [1] "data/interim/annotations/example_sirius_5.zip"
#> 
#> $data$interim$annotations$example_sirius$v6
#> [1] "data/interim/annotations/example_sirius_6.zip"
#> 
#> 
#> 
#> $data$interim$features
#> $data$interim$features$path
#> [1] "data/interim/features"
#> 
#> 
#> $data$interim$libraries
#> $data$interim$libraries$path
#> [1] "data/interim/libraries"
#> 
#> $data$interim$libraries$adducts
#> $data$interim$libraries$adducts$path
#> [1] "data/interim/libraries/adducts"
#> 
#> $data$interim$libraries$adducts$neg
#> [1] "data/interim/libraries/adducts/neg.tsv.gz"
#> 
#> $data$interim$libraries$adducts$pos
#> [1] "data/interim/libraries/adducts/pos.tsv.gz"
#> 
#> 
#> $data$interim$libraries$sop
#> $data$interim$libraries$sop$path
#> [1] "data/interim/libraries/sop"
#> 
#> $data$interim$libraries$sop$closed
#> [1] "data/interim/libraries/sop/closed_prepared.tsv.gz"
#> 
#> $data$interim$libraries$sop$hmdb
#> [1] "data/interim/libraries/sop/hmdb_prepared.tsv.gz"
#> 
#> $data$interim$libraries$sop$hmdb_minimal
#> [1] "data/interim/libraries/sop/hmdb_minimal.tsv.gz"
#> 
#> $data$interim$libraries$sop$lotus
#> [1] "data/interim/libraries/sop/lotus_prepared.tsv.gz"
#> 
#> $data$interim$libraries$sop$merged
#> $data$interim$libraries$sop$merged$path
#> [1] "data/interim/libraries/sop/merged"
#> 
#> $data$interim$libraries$sop$merged$keys
#> [1] "data/interim/libraries/sop/merged/keys.tsv.gz"
#> 
#> $data$interim$libraries$sop$merged$organisms
#> $data$interim$libraries$sop$merged$organisms$path
#> [1] "data/interim/libraries/sop/merged/organisms"
#> 
#> $data$interim$libraries$sop$merged$organisms$names
#> [1] "data/interim/libraries/sop/merged/organisms/names.tsv.gz"
#> 
#> $data$interim$libraries$sop$merged$organisms$taxonomies
#> $data$interim$libraries$sop$merged$organisms$taxonomies$path
#> [1] "data/interim/libraries/sop/merged/organisms/taxonomies"
#> 
#> $data$interim$libraries$sop$merged$organisms$taxonomies$ott
#> [1] "data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz"
#> 
#> 
#> 
#> $data$interim$libraries$sop$merged$structures
#> $data$interim$libraries$sop$merged$structures$path
#> [1] "data/interim/libraries/sop/merged/structures"
#> 
#> $data$interim$libraries$sop$merged$structures$stereo
#> [1] "data/interim/libraries/sop/merged/structures/stereo.tsv.gz"
#> 
#> $data$interim$libraries$sop$merged$structures$metadata
#> [1] "data/interim/libraries/sop/merged/structures/metadata.tsv.gz"
#> 
#> $data$interim$libraries$sop$merged$structures$names
#> [1] "data/interim/libraries/sop/merged/structures/names.tsv.gz"
#> 
#> $data$interim$libraries$sop$merged$structures$taxonomies
#> $data$interim$libraries$sop$merged$structures$taxonomies$path
#> [1] "data/interim/libraries/sop/merged/structures/taxonomies"
#> 
#> $data$interim$libraries$sop$merged$structures$taxonomies$cla
#> [1] "data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz"
#> 
#> $data$interim$libraries$sop$merged$structures$taxonomies$npc
#> [1] "data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz"
#> 
#> 
#> 
#> 
#> 
#> $data$interim$libraries$spectra
#> $data$interim$libraries$spectra$path
#> [1] "data/interim/libraries/spectra"
#> 
#> $data$interim$libraries$spectra$exp
#> $data$interim$libraries$spectra$exp$path
#> [1] "data/interim/libraries/spectra/exp"
#> 
#> $data$interim$libraries$spectra$exp$mona
#> $data$interim$libraries$spectra$exp$mona$pos
#> [1] "data/interim/libraries/spectra/exp/mona_pos.rds"
#> 
#> $data$interim$libraries$spectra$exp$mona$neg
#> [1] "data/interim/libraries/spectra/exp/mona_neg.rds"
#> 
#> 
#> 
#> $data$interim$libraries$spectra$is
#> $data$interim$libraries$spectra$is$path
#> [1] "data/interim/libraries/spectra/is"
#> 
#> $data$interim$libraries$spectra$is$hmdb
#> $data$interim$libraries$spectra$is$hmdb$pos
#> [1] "data/interim/libraries/spectra/is/hmdb_pos.rds"
#> 
#> $data$interim$libraries$spectra$is$hmdb$neg
#> [1] "data/interim/libraries/spectra/is/hmdb_neg.rds"
#> 
#> 
#> $data$interim$libraries$spectra$is$lotus
#> $data$interim$libraries$spectra$is$lotus$pos
#> [1] "data/interim/libraries/spectra/is/lotus_pos.rds"
#> 
#> $data$interim$libraries$spectra$is$lotus$neg
#> [1] "data/interim/libraries/spectra/is/lotus_neg.rds"
#> 
#> 
#> 
#> 
#> 
#> $data$interim$params
#> $data$interim$params$path
#> [1] "data/interim/params"
#> 
#> 
#> $data$interim$taxa
#> $data$interim$taxa$path
#> [1] "data/interim/taxa"
#> 
#> 
#> 
#> $data$processed
#> $data$processed$path
#> [1] "data/processed"
#> 
#> 
#> $data$source
#> $data$source$path
#> [1] "data/source"
#> 
#> $data$source$features
#> [1] "data/source/example_features.csv"
#> 
#> $data$source$metadata
#> [1] "data/source/example_metadata.tsv"
#> 
#> $data$source$spectra
#> [1] "data/source/example_spectra.mgf"
#> 
#> $data$source$benchmark
#> $data$source$benchmark$path
#> [1] "data/source/benchmark"
#> 
#> $data$source$benchmark$cleaned
#> [1] "data/interim/benchmark/cleaned_libraries_matchms/results_library_cleaning/cleaned_spectra.mgf"
#> 
#> $data$source$benchmark$mgf
#> $data$source$benchmark$mgf$neg
#> [1] "data/interim/benchmark/benchmark_neg.mgf"
#> 
#> $data$source$benchmark$mgf$pos
#> [1] "data/interim/benchmark/benchmark_pos.mgf"
#> 
#> 
#> $data$source$benchmark$zip
#> [1] "data/source/benchmark/cleaned_libraries_matchms.zip"
#> 
#> 
#> $data$source$libraries
#> $data$source$libraries$path
#> [1] "data/source/libraries"
#> 
#> $data$source$libraries$rt
#> $data$source$libraries$rt$path
#> [1] "data/source/libraries/rt"
#> 
#> $data$source$libraries$rt$example_mini
#> [1] "data/source/libraries/rt/example_lib_mini_rt.tsv"
#> 
#> 
#> $data$source$libraries$sop
#> $data$source$libraries$sop$path
#> [1] "data/source/libraries/sop"
#> 
#> $data$source$libraries$sop$closed
#> [1] "../lotus-processor/data/processed/230224_closed_metadata.csv.gz"
#> 
#> $data$source$libraries$sop$ecmdb
#> [1] "data/source/libraries/sop/ecmdb.json.zip"
#> 
#> $data$source$libraries$sop$hmdb
#> [1] "data/source/libraries/sop/hmdb/structures.zip"
#> 
#> $data$source$libraries$sop$lotus
#> [1] "data/source/libraries/sop/lotus.csv.gz"
#> 
#> 
#> $data$source$libraries$spectra
#> $data$source$libraries$spectra$path
#> [1] "data/source/libraries/spectra"
#> 
#> $data$source$libraries$spectra$exp
#> $data$source$libraries$spectra$exp$path
#> [1] "data/source/libraries/spectra/exp"
#> 
#> $data$source$libraries$spectra$exp$mona_lcmsms
#> [1] "data/source/libraries/spectra/exp/MoNA-export-LC-MS-MS_Spectra.sdf"
#> 
#> $data$source$libraries$spectra$exp$with_rt
#> [1] "data/source/libraries/spectra/exp/spectral_lib_mini_with_rt.mgf"
#> 
#> 
#> $data$source$libraries$spectra$is
#> $data$source$libraries$spectra$is$hmdb
#> [1] "data/source/libraries/spectra/is/hmdb_predicted_msms_spectra.zip"
#> 
#> $data$source$libraries$spectra$is$lotus
#> $data$source$libraries$spectra$is$lotus$pos
#> [1] "data/source/libraries/spectra/is/isdb_pos.mgf"
#> 
#> $data$source$libraries$spectra$is$lotus$neg
#> [1] "data/source/libraries/spectra/is/isdb_neg.mgf"
#> 
#> 
#> 
#> 
#> 
#> 
#> 
#> $doc
#> $doc$path
#> [1] "doc"
#> 
#> 
#> $img
#> $img$path
#> [1] "img"
#> 
#> 
#> $inst
#> $inst$path
#> [1] "inst"
#> 
#> $inst$scripts
#> $inst$scripts$path
#> [1] "scripts"
#> 
#> $inst$scripts$docopt
#> $inst$scripts$docopt$path
#> [1] "scripts/docopt"
#> 
#> 
#> 
#> 
#> $gnps
#> $gnps$example
#> [1] "41c6068e905d482db5698ad81d145d7c"
#> 
#> $gnps$example2
#> [1] "958d60d32e0c43bc9a06798b744f41c7"
#> 
#> 
#> $params
#> $params$path
#> [1] "params"
#> 
#> $params$default
#> $params$default$path
#> [1] "params/default"
#> 
#> $params$default$annotate
#> $params$default$annotate$masses
#> [1] "params/default/annotate_masses.yaml"
#> 
#> $params$default$annotate$spectra
#> [1] "params/default/annotate_spectra.yaml"
#> 
#> 
#> $params$default$create
#> $params$default$create$components
#> [1] "params/default/create_components.yaml"
#> 
#> $params$default$create$edges
#> $params$default$create$edges$spectra
#> [1] "params/default/create_edges_spectra.yaml"
#> 
#> 
#> 
#> $params$default$filter
#> $params$default$filter$annotations
#> [1] "params/default/filter_annotations.yaml"
#> 
#> 
#> $params$default$prepare
#> $params$default$prepare$features
#> $params$default$prepare$features$components
#> [1] "params/default/prepare_features_components.yaml"
#> 
#> $params$default$prepare$features$edges
#> [1] "params/default/prepare_features_edges.yaml"
#> 
#> $params$default$prepare$features$tables
#> [1] "params/default/prepare_features_tables.yaml"
#> 
#> 
#> $params$default$prepare$libraries
#> $params$default$prepare$libraries$rt
#> [1] "params/default/prepare_libraries_rt.yaml"
#> 
#> $params$default$prepare$libraries$sop
#> $params$default$prepare$libraries$sop$closed
#> [1] "params/default/prepare_libraries_sop_closed.yaml"
#> 
#> $params$default$prepare$libraries$sop$ecmdb
#> [1] "params/default/prepare_libraries_sop_ecmdb.yaml"
#> 
#> $params$default$prepare$libraries$sop$hmdb
#> [1] "params/default/prepare_libraries_sop_hmdb.yaml"
#> 
#> $params$default$prepare$libraries$sop$lotus
#> [1] "params/default/prepare_libraries_sop_lotus.yaml"
#> 
#> $params$default$prepare$libraries$sop$merged
#> [1] "params/default/prepare_libraries_sop_merged.yaml"
#> 
#> 
#> $params$default$prepare$libraries$spectra
#> [1] "params/default/prepare_libraries_spectra.yaml"
#> 
#> 
#> $params$default$prepare$annotations
#> $params$default$prepare$annotations$gnps
#> [1] "params/default/prepare_annotations_gnps.yaml"
#> 
#> $params$default$prepare$annotations$sirius
#> [1] "params/default/prepare_annotations_sirius.yaml"
#> 
#> $params$default$prepare$annotations$spectra
#> [1] "params/default/prepare_annotations_spectra.yaml"
#> 
#> 
#> $params$default$prepare$taxa
#> [1] "params/default/prepare_taxa.yaml"
#> 
#> 
#> $params$default$weight
#> $params$default$weight$annotations
#> [1] "params/default/weight_annotations.yaml"
#> 
#> 
#> 
#> $params$prepare_params
#> [1] "params/prepare_params.yaml"
#> 
#> $params$prepare_params_advanced
#> [1] "params/prepare_params_advanced.yaml"
#> 
#> $params$user
#> $params$user$path
#> [1] "params/user"
#> 
#> $params$user$annotate
#> $params$user$annotate$masses
#> [1] "params/user/annotate_masses.yaml"
#> 
#> $params$user$annotate$spectra
#> [1] "params/user/annotate_spectra.yaml"
#> 
#> 
#> $params$user$create
#> $params$user$create$components
#> [1] "params/user/create_components.yaml"
#> 
#> $params$user$create$edges
#> $params$user$create$edges$spectra
#> [1] "params/user/create_edges_spectra.yaml"
#> 
#> 
#> 
#> $params$user$filter
#> $params$user$filter$annotations
#> [1] "params/user/filter_annotations.yaml"
#> 
#> 
#> $params$user$prepare
#> $params$user$prepare$features
#> $params$user$prepare$features$components
#> [1] "params/user/prepare_features_components.yaml"
#> 
#> $params$user$prepare$features$edges
#> [1] "params/user/prepare_features_edges.yaml"
#> 
#> $params$user$prepare$features$tables
#> [1] "params/user/prepare_features_tables.yaml"
#> 
#> 
#> $params$user$prepare$libraries
#> $params$user$prepare$libraries$rt
#> [1] "params/user/prepare_libraries_rt.yaml"
#> 
#> $params$user$prepare$libraries$sop
#> $params$user$prepare$libraries$sop$closed
#> [1] "params/user/prepare_libraries_sop_closed.yaml"
#> 
#> $params$user$prepare$libraries$sop$ecmdb
#> [1] "params/user/prepare_libraries_sop_ecmdb.yaml"
#> 
#> $params$user$prepare$libraries$sop$hmdb
#> [1] "params/user/prepare_libraries_sop_hmdb.yaml"
#> 
#> $params$user$prepare$libraries$sop$lotus
#> [1] "params/user/prepare_libraries_sop_lotus.yaml"
#> 
#> $params$user$prepare$libraries$sop$merged
#> [1] "params/user/prepare_libraries_sop_merged.yaml"
#> 
#> 
#> $params$user$prepare$libraries$spectra
#> [1] "params/user/prepare_libraries_spectra.yaml"
#> 
#> 
#> $params$user$prepare$annotations
#> $params$user$prepare$annotations$gnps
#> [1] "params/user/prepare_annotations_gnps.yaml"
#> 
#> $params$user$prepare$annotations$sirius
#> [1] "params/user/prepare_annotations_sirius.yaml"
#> 
#> $params$user$prepare$annotations$spectra
#> [1] "params/user/prepare_annotations_spectra.yaml"
#> 
#> 
#> $params$user$prepare$taxa
#> [1] "params/user/prepare_taxa.yaml"
#> 
#> 
#> $params$user$weight
#> $params$user$weight$annotations
#> [1] "params/user/weight_annotations.yaml"
#> 
#> 
#> 
#> 
#> $tests
#> $tests$mode
#> [1] FALSE
#> 
#> $tests$path
#> [1] "tests"
#> 
#> 
#> $urls
#> $urls$benchmarking_set
#> [1] "https://zenodo.org/records/10160791/files/cleaned_libraries_matchms.zip?download=1"
#> 
#> $urls$examples
#> $urls$examples$features
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_features.csv"
#> 
#> $urls$examples$lib_mini
#> $urls$examples$lib_mini$rt
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_lib_mini_rt.tsv"
#> 
#> 
#> $urls$examples$metadata
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_metadata.tsv"
#> 
#> $urls$examples$sirius
#> $urls$examples$sirius$v5
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_sirius_5.zip"
#> 
#> $urls$examples$sirius$v6
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_sirius_6.zip"
#> 
#> 
#> $urls$examples$spectra
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_spectra.mgf"
#> 
#> $urls$examples$spectra_mini
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_spectra_mini.mgf"
#> 
#> $urls$examples$spectra_ms1
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/example_spectra_ms1.mgf"
#> 
#> $urls$examples$spectral_lib
#> $urls$examples$spectral_lib$neg
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/lotus_neg.rds"
#> 
#> $urls$examples$spectral_lib$pos
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/lotus_pos.rds"
#> 
#> 
#> $urls$examples$spectral_lib_mini
#> $urls$examples$spectral_lib_mini$neg
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/spectral_lib_mini_neg.mgf"
#> 
#> $urls$examples$spectral_lib_mini$pos
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/spectral_lib_mini_pos.mgf"
#> 
#> $urls$examples$spectral_lib_mini$with_rt
#> [1] "https://github.com/taxonomicallyinformedannotation/tima-example-files/raw/main/spectral_lib_mini_with_rt.mgf"
#> 
#> 
#> 
#> $urls$ecmdb
#> $urls$ecmdb$metabolites
#> [1] "https://ecmdb.ca/download/ecmdb.json.zip"
#> 
#> 
#> $urls$hmdb
#> $urls$hmdb$metabolites
#> [1] "https://hmdb.ca/system/downloads/current/hmdb_metabolites.zip"
#> 
#> $urls$hmdb$spectra
#> $urls$hmdb$spectra$predicted
#> [1] "https://hmdb.ca/system/downloads/current/spectral_data/spectra_xml/hmdb_predicted_msms_spectra.zip"
#> 
#> 
#> $urls$hmdb$structures
#> [1] "https://hmdb.ca/system/downloads/current/structures.zip"
#> 
#> 
#> $urls$lotus
#> $urls$lotus$doi
#> [1] "10.5281/zenodo.5794106"
#> 
#> $urls$lotus$pattern
#> [1] "frozen_metadata.csv.gz"
#> 
#> $urls$lotus$metadata_doi
#> [1] "10.5281/zenodo.6378223"
#> 
#> $urls$lotus$metadata_pattern
#> $urls$lotus$metadata_pattern$organisms
#> [1] "organism_metadata.tsv.gz"
#> 
#> $urls$lotus$metadata_pattern$references
#> [1] "reference_metadata.tsv.gz"
#> 
#> $urls$lotus$metadata_pattern$structures
#> [1] "structure_metadata.tsv.gz"
#> 
#> 
#> 
#> $urls$lotus_isdb
#> $urls$lotus_isdb$doi
#> [1] "10.5281/zenodo.5607185"
#> 
#> $urls$lotus_isdb$pattern
#> $urls$lotus_isdb$pattern$pos
#> [1] "isdb_pos.mgf"
#> 
#> $urls$lotus_isdb$pattern$neg
#> [1] "isdb_neg.mgf"
#> 
#> 
#> 
#> $urls$massbank
#> $urls$massbank$file
#> [1] "MassBank_NIST.msp"
#> 
#> $urls$massbank$url
#> [1] "https://github.com/MassBank/MassBank-data/releases/download"
#> 
#> $urls$massbank$version
#> [1] 2024.06
#> 
#> 
#>