Mercurial > repos > siwaa > carboseq_s

annotate run.r @ 9:2af4b1e46d90 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/0376c8590ba7b401f91db9be50a49e03cf5044fb/toos/CarboSeqSimulator commit 0376c8590ba7b401f91db9be50a49e03cf5044fb-dirty"
author siwaa
date Tue, 17 Sep 2024 10:41:39 +0000
parents 5fdc9d0c223b
children de71663fbce4
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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2 # help : Rscript % --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=~/CSCL/src/csoprapreprocessor/inst/extdata/carboseq/set001/
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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4 # Function to parse command-line arguments
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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5 parse_args <- function() {
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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6 args <- commandArgs(trailingOnly = TRUE)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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8 # Default values for optional parameters
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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9 url <- "https://coby.infosol.inrae.fr:8080/semantify/"
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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10 srcDir <- NULL
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
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11 # srcDirOutput <- NULL
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
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12 part <- "modeltoolbox_sem_remote"
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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13 DS <- T
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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14 NBCores <- 1
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
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15 semPath <- "."
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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16 # Parse arguments
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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17 for (arg in args) {
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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19 if (grepl("^--url=", arg)) {
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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20 url <- sub("^--url=", "", arg)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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21 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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23 if (grepl("^--srcDir=", arg)) {
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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24 srcDir <- sub("^--srcDir=", "", arg)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
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25 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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27 # if (grepl("^--srcDirOutput=", arg)) {
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
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28 # srcDirOutput <- sub("^--srcDirOutput=", "", arg)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
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29 # }
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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30 if (grepl("^--part=", arg)) {
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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31 part <- sub("^--part=", "", arg)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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32 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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34 if (grepl("^--DS=", arg)) {
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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35 DS <- ifelse(sub("^--DS=", "", arg) == "TRUE", TRUE, FALSE)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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36 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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38 if (grepl("^--NBCores=", arg)) {
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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39 NBCores <- as.numeric(sub("^--NBCores=", "", arg))
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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40 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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42 if (grepl("^--srcOut=", arg)) {
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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43 srcOut <- sub("^--srcOut=", "", arg)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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44 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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46 if (grepl("^--semPath=", arg)) {
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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47 semPath <- sub("^--semPath=", "", arg)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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48 }
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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49 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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51 list( url = url, srcDir = srcDir, part = part, DS = DS,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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52 NBCores = NBCores, srcOut = srcOut, semPath = semPath )
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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53 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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55 argus <- parse_args()
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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57 url <- argus[["url"]]
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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58 srcDir <- argus[["srcDir"]]
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
59 # srcDirOutput <- argus[["srcDirOutput"]]
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
60 part <- argus[["part"]]
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
61 DS <- argus[["DS"]]
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
62 NBCores <- argus[["NBCores"]]
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
63
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
64 srcOut <- argus[["srcOut"]]
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
65
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
66 semPath <- argus[["semPath"]]
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
67
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
68 if (!endsWith(srcOut, "/")) {
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
69 srcOut <- paste0(srcOut, "/")
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
70 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
71
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
72 #if (is.null(srcDirOutput)) {
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
73 # srcDirOutput <- srcDir
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
74 # }
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
75
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
76 # url="https://147.100.203.110/semantify "
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
77 # srcDir="~/tmp/testFiles/400Sites/"
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
78 # part="modeltoolbox"
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
79 # part="csoprapreprocessor"
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
80 # DS=TRUE
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
81 # NBCores=10
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
82
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
83 # MTB{{{
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
84 if (part == "modeltoolbox") {
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
85 f0 <- function(){
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
86 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
87 preprocessorInputs = ppi)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
88 modeltoolbox::runSims(maxCores = NBCores)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
89 res <- modeltoolbox::readSocForcingsResults()
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
90 fileName <- "resRun.RData"
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
91 filePath <- file.path(srcOut, fileName)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
92 save(res, file = filePath)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
93 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
94 }
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
95 #}}}
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents:
diff changeset
96
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
97 if (part == "modeltoolbox_sem_local") {
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
98 DS <- F
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
99 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
100 f0 <- function(){
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
101 path <- this.path::this.dir()
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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parents: 4
diff changeset
102 print(path)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
103 csopratools::semantify(
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
104 inputDir = srcDir,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
105 outputDir = srcDir,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
106 name = "carboseq",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
107 # use = "service",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
108 URL = url,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
109 use = "java",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
110 semantifierRootPath = semPath,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
111 extFileNames = paste0(c("crop", "soil", "units"), ".csv")
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
112 )
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
113 print("between semantify and load")
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
114
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
115 ppi$srcDirOutput <- NULL # Hack
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
116
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
117 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 4
diff changeset
118 preprocessorInputs = ppi)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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119 print("between load an sim")
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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120 modeltoolbox::runSims(maxCores = NBCores)
8
5fdc9d0c223b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/43e7f4ebfe4e552bf684936df0a050cb6def5aab/toos/CarboSeqSimulator commit 43e7f4ebfe4e552bf684936df0a050cb6def5aab-dirty"
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121 res <- modeltoolbox::getYearlySOCResults()
5fdc9d0c223b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/43e7f4ebfe4e552bf684936df0a050cb6def5aab/toos/CarboSeqSimulator commit 43e7f4ebfe4e552bf684936df0a050cb6def5aab-dirty"
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122 # res <- modeltoolbox::readSocForcingsResults()
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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123 fileName <- "resRun.RData"
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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124 filePath <- file.path(srcOut, fileName)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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125 save(res, file = filePath)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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126 }
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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127 }
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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128
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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129 if (part == "modeltoolbox_sem_remote") {
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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130 DS <- F
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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131 print("Setting DS to F. Will semantify outside of the csoprapreprocessor functions")
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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132 f0 <- function(){
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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133 path <- this.path::this.dir()
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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134 print(path)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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diff changeset
135 setwd(path)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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136 setwd("../..")
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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137 csopratools::semantify(
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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138 inputDir = srcDir,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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139 outputDir = srcDir,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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140 name = "carboseq",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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141 use = "service",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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142 URL = url,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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143 extFileNames = paste0(c("crop", "soil", "units"), ".csv")
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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144 )
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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145
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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146 # ppi$srcDirOutput <- NULL # Hack
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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147
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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148 modeltoolbox::loadCSVs(maxCores = NBCores, cinputCalculator = "cinest",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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149 preprocessorInputs = ppi)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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150 modeltoolbox::runSims(maxCores = NBCores)
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5fdc9d0c223b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/43e7f4ebfe4e552bf684936df0a050cb6def5aab/toos/CarboSeqSimulator commit 43e7f4ebfe4e552bf684936df0a050cb6def5aab-dirty"
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151 res <- modeltoolbox::getYearlySOCResults()
5fdc9d0c223b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/43e7f4ebfe4e552bf684936df0a050cb6def5aab/toos/CarboSeqSimulator commit 43e7f4ebfe4e552bf684936df0a050cb6def5aab-dirty"
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152 # res <- modeltoolbox::readSocForcingsResults()
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366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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153 fileName <- "resRun.RData"
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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154 filePath <- file.path(srcOut, fileName)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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155 save(res, file = filePath)
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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156 }
4
a069fc43b0b1 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
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157 }
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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158
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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159 ppi <- list(
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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160 weatherRetrievalMethod = "service",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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161 srcDir = srcDir,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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162 # srcDirOutput = srcDirOutput,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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163 doSemantify = DS,
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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164 weatherRetrievalURL = "https://coby.infosol.inrae.fr:8080/climate",
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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165 semantifierServiceURL = url
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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166 )
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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167
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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168
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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169 print(url)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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170 print(srcDir)
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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171 # print(srcDirOutput)
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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172 print(srcOut)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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173 print(DS)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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174 print(NBCores)
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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175 print(f0)
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
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176
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
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177 f0()