Mercurial > repos > ppericard > mixomics_blocksplsda

annotate computeMatSimilarity_wrapper.R @ 3:0a3c83f2197a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author ppericard
date Fri, 25 Oct 2019 07:10:59 -0400
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1 #!/usr/bin/env Rscript
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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3 # Setup R error handling to go to stderr
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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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.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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9 ## Get parameters ##
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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10 suppressPackageStartupMessages(require(argparse))
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12 parser <- ArgumentParser(description='Run the computeMatSimilarity function')
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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15 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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17 args <- parser$parse_args()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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19 ## Print parameters
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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20 print("Input RData:")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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21 print(args$input_rdata)
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22 print("Output RData:")
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23 print(args$output_rdata)
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25 ## Loading libraries
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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26 # suppressPackageStartupMessages(require(mixOmics))
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28 # R script call
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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29 source_local <- function(fname)
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30 {
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31 argv <- commandArgs(trailingOnly = FALSE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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32 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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33 source(paste(base_dir, fname, sep="/"))
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34 }
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35 ## Loading local functions
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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36 source_local("Integration_block_splsda_fonc.R")
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38 load(args$input_rdata)
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40 liste_res_matSimilarity_group = compute_matSimilarity(liste_dataframe_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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42 liste_matSimilarity_group = liste_res_matSimilarity_group$liste_matSimilarity_group
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43 comp = liste_res_matSimilarity_group$comp
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45 save(liste_matSimilarity_group,
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46 comp,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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47 file = args$output_rdata)