Mercurial > repos > workflow4metabolomics > w4mconcatenate

comparison concatenation_wrapper.R @ 0:c577f13705f2 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
author workflow4metabolomics
date Wed, 10 Jul 2024 15:20:11 +0000
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-1:000000000000 0:c577f13705f2
1 rm(list = ls())
2 #Chargement des library et des ressources
3
4 library("W4MRUtils")
5 library(dplyr)
6
7
8 source_local("concatenation.R")
9 source_local("fonctions_auxiliaires.R")
10
11
12 para <- W4MRUtils::parse_args(args = commandArgs())
13
14
15 cat("\nJob starting time:\n", format(Sys.time(), "%a %d %b %Y %X"),
16 "\n\n--------------------------------------------------------------------",
17 "\nParameters used by the 'W4M concatenate' tool:\n\n")
18 print(para)
19 cat("--------------------------------------------------------------------\n\n")
20
21
22 #Lancement de l'outil
23
24 A <- W4MRUtils::import2(para$dataMatrix_1, para$metadata_1, para$type, disable_comm = FALSE)
25 B <- W4MRUtils::import2(para$dataMatrix_2, para$metadata_2, para$type, disable_comm = FALSE)
26
27 DM1 <- A$dataMatrix
28 M1 <- A$metadata
29
30 DM2 <- B$dataMatrix
31 M2 <- B$metadata
32
33
34 result_tables <- concat(DM1, M1, DM2, M2, para$type, para$tab1, para$tab2, para$concatenation, para$choice_keep, para$keep)
35
36 write.table(result_tables[[1]], file = para$metadata_out, sep = "\t", row.names = FALSE, quote = FALSE)
37 write.table(result_tables[[2]], file = para$dataMatrix_1_out, sep = "\t", row.names = FALSE, quote = FALSE)
38 write.table(result_tables[[3]], file = para$dataMatrix_2_out, sep = "\t", row.names = FALSE, quote = FALSE)
39
40 cat("\n--------------------------------------------------------------------",
41 "\nInformation about R (version, Operating System, attached or loaded packages):\n\n")
42 sessionInfo()
43 cat("--------------------------------------------------------------------\n",
44 "\nJob ending time:\n", format(Sys.time(), "%a %d %b %Y %X"))