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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents c8533e9298e5
children
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c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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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$output_rdata)
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25 ## Loading libraries
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26 # suppressPackageStartupMessages(require(mixOmics))
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28 # R script call
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29 source_local <- function(fname)
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30 {
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31 argv <- commandArgs(trailingOnly = FALSE)
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32 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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33 source(paste(base_dir, fname, sep="/"))
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34 }
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36 ## Loading local functions
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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37 suppressPackageStartupMessages(require(visCorVar))
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39 # Loading input Rdata file
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40 # loads res_matCorAddVar object
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41 load(args$input_rdata)
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43 # Run main function
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44 res_compute_mat_similarity = computeMatSimilarity(res_matCorAddVar = res_matCorAddVar)
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46 liste_mat_similarity_group = res_compute_mat_similarity$liste_mat_similarity_group
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47 res_matCorAddVar = res_compute_mat_similarity$res_matCorAddVar
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49 save(res_compute_mat_similarity,
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50 file = args$output_rdata)