Mercurial > repos > ppericard > viscorvar

annotate computeMatSimilarity_wrapper.R @ 1:e93350dc99f1 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author ppericard
date Thu, 15 Oct 2020 12:22:25 +0000
parents d0b77b926863
children
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1 #!/usr/bin/env Rscript
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3 # Setup R error handling to go to stderr
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4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 ## Get parameters ##
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10 suppressPackageStartupMessages(require(argparse))
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12 parser <- ArgumentParser(description='Run the computeMatSimilarity function')
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14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
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15 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")
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17 args <- parser$parse_args()
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19 ## Print parameters
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20 print("Input RData:")
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21 print(args$input_rdata)
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22 print("Output RData:")
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23 print(args$output_rdata)
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25 ## Loading libraries
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26 # suppressPackageStartupMessages(require(mixOmics))
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28 # R script call
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29 source_local <- function(fname)
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30 {
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31 argv <- commandArgs(trailingOnly = FALSE)
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32 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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33 source(paste(base_dir, fname, sep="/"))
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34 }
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36 ## Loading local functions
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37 # source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R")
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38 install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.5.tar.gz", repos=NULL)
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39 suppressPackageStartupMessages(require(visCorVar))
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40 print("visCorVar has been loaded")
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42 # Loading input Rdata file
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43 # loads res_matCorAddVar object
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44 load(args$input_rdata)
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46 # Run main function
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47 res_compute_mat_similarity = computeMatSimilarity(res_matCorAddVar = res_matCorAddVar)
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49 liste_mat_similarity_group = res_compute_mat_similarity$liste_mat_similarity_group
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50 res_matCorAddVar = res_compute_mat_similarity$res_matCorAddVar
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52 save(res_compute_mat_similarity,
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53 file = args$output_rdata)