view computeMatSimilarity_wrapper.R @ 1:e93350dc99f1 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"

#!/usr/bin/env Rscript

# Setup R error handling to go to stderr
options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

## Get parameters ##
suppressPackageStartupMessages(require(argparse))

parser <- ArgumentParser(description='Run the computeMatSimilarity function')

parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")

args <- parser$parse_args()

## Print parameters
print("Input RData:")
print(args$input_rdata)
print("Output RData:")
print(args$output_rdata)

## Loading libraries
# suppressPackageStartupMessages(require(mixOmics))

# R script call
source_local <- function(fname)
{
    argv <- commandArgs(trailingOnly = FALSE)
    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
    source(paste(base_dir, fname, sep="/"))
}

## Loading local functions
# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R")
install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.5.tar.gz", repos=NULL)
suppressPackageStartupMessages(require(visCorVar))
print("visCorVar has been loaded")

# Loading input Rdata file
# loads res_matCorAddVar object
load(args$input_rdata)

# Run main function
res_compute_mat_similarity = computeMatSimilarity(res_matCorAddVar = res_matCorAddVar)

liste_mat_similarity_group  = res_compute_mat_similarity$liste_mat_similarity_group
res_matCorAddVar = res_compute_mat_similarity$res_matCorAddVar

save(res_compute_mat_similarity,
     file = args$output_rdata)