Mercurial > repos > recetox > recetox_aplcms_hybrid

annotate main.R @ 5:3a8864093eac draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
author recetox
date Fri, 18 Jun 2021 20:51:55 +0000
parents
children 27853894eeac
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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diff changeset
1 library(recetox.aplcms)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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3 save_extracted_features <- function(df, filename) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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4 df <- as.data.frame(df)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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5 columns <- c("mz", "pos", "sd1", "sd2", "area")
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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6 arrow::write_parquet(df[columns], filename)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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7 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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9 save_feature_sample_table <- function(df, filename) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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10 columns <- c("feature", "mz", "rt", "sample", "sample_rt", "sample_intensity")
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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11 arrow::write_parquet(df[columns], filename)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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12 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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14 known_table_columns <- function() {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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15 c("chemical_formula", "HMDB_ID", "KEGG_compound_ID", "mass", "ion.type",
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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16 "m.z", "Number_profiles_processed", "Percent_found", "mz_min", "mz_max",
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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17 "RT_mean", "RT_sd", "RT_min", "RT_max", "int_mean(log)", "int_sd(log)",
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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18 "int_min(log)", "int_max(log)")
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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19 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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21 save_known_table <- function(df, filename) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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22 columns <- known_table_columns()
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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23 arrow::write_parquet(df[columns], filename)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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24 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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26 read_known_table <- function(filename) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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27 arrow::read_parquet(filename, col_select = known_table_columns())
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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28 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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30 save_pairing <- function(df, filename) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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31 write.table(df, filename, row.names = FALSE, col.names = c("new", "old"))
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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32 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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34 save_all_extracted_features <- function(dfs, filenames) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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35 filenames <- tools::file_path_sans_ext(basename(filenames))
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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36 filenames <- paste0(filenames, ".parquet")
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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37 filenames <- file.path("extracted", filenames)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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38 dir.create("extracted")
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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39 mapply(save_extracted_features, dfs, filenames)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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40 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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42 save_all_corrected_features <- function(dfs, filenames) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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43 filenames <- tools::file_path_sans_ext(basename(filenames))
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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44 filenames <- paste0(filenames, ".parquet")
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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45 filenames <- file.path("corrected", filenames)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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46 dir.create("corrected")
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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47 mapply(save_extracted_features, dfs, filenames)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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48 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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50 unsupervised_main <- function(sample_files, aligned_file, recovered_file, ...) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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51 sample_files <- sort_samples_by_acquisition_number(sample_files)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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53 res <- unsupervised(filenames = sample_files, ...)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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55 save_all_extracted_features(res$extracted_features, sample_files)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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56 save_all_corrected_features(res$corrected_features, sample_files)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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58 save_feature_sample_table(res$aligned_feature_sample_table, aligned_file)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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59 save_feature_sample_table(res$recovered_feature_sample_table, recovered_file)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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60 }
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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62 hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, ...) {
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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63 sample_files <- sort_samples_by_acquisition_number(sample_files)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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65 known <- read_known_table(known_table_file)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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66 res <- hybrid(filenames = sample_files, known_table = known, ...)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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68 save_known_table(res$updated_known_table, updated_known_table_file)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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69 save_pairing(res$features_known_table_pairing, pairing_file)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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71 save_all_extracted_features(res$extracted_features, sample_files)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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72 save_all_corrected_features(res$corrected_features, sample_files)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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74 save_feature_sample_table(res$aligned_feature_sample_table, aligned_file)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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75 save_feature_sample_table(res$recovered_feature_sample_table, recovered_file)
3a8864093eac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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76 }