Mercurial > repos > workflow4metabolomics > w4mconcatenate
annotate concatenation_wrapper.R @ 0:c577f13705f2 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
| author | workflow4metabolomics |
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| date | Wed, 10 Jul 2024 15:20:11 +0000 |
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| rev | line source |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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1 rm(list = ls()) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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2 #Chargement des library et des ressources |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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3 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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4 library("W4MRUtils") |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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5 library(dplyr) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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6 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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7 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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8 source_local("concatenation.R") |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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9 source_local("fonctions_auxiliaires.R") |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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11 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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12 para <- W4MRUtils::parse_args(args = commandArgs()) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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15 cat("\nJob starting time:\n", format(Sys.time(), "%a %d %b %Y %X"), |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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16 "\n\n--------------------------------------------------------------------", |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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17 "\nParameters used by the 'W4M concatenate' tool:\n\n") |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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18 print(para) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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19 cat("--------------------------------------------------------------------\n\n") |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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20 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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21 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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22 #Lancement de l'outil |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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23 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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24 A <- W4MRUtils::import2(para$dataMatrix_1, para$metadata_1, para$type, disable_comm = FALSE) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
changeset
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25 B <- W4MRUtils::import2(para$dataMatrix_2, para$metadata_2, para$type, disable_comm = FALSE) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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26 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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27 DM1 <- A$dataMatrix |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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28 M1 <- A$metadata |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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29 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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30 DM2 <- B$dataMatrix |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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31 M2 <- B$metadata |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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34 result_tables <- concat(DM1, M1, DM2, M2, para$type, para$tab1, para$tab2, para$concatenation, para$choice_keep, para$keep) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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35 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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36 write.table(result_tables[[1]], file = para$metadata_out, sep = "\t", row.names = FALSE, quote = FALSE) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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37 write.table(result_tables[[2]], file = para$dataMatrix_1_out, sep = "\t", row.names = FALSE, quote = FALSE) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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38 write.table(result_tables[[3]], file = para$dataMatrix_2_out, sep = "\t", row.names = FALSE, quote = FALSE) |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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39 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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40 cat("\n--------------------------------------------------------------------", |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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41 "\nInformation about R (version, Operating System, attached or loaded packages):\n\n") |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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42 sessionInfo() |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
changeset
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43 cat("--------------------------------------------------------------------\n", |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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44 "\nJob ending time:\n", format(Sys.time(), "%a %d %b %Y %X")) |