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annotate ExeFilteringRareLowabundSPGalaxy.r @ 1:fd0687e91bf6 draft default tip

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"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
author ecology
date Mon, 11 May 2020 17:44:48 -0400
parents 2e45ae3b297a
children
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2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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1 #!/usr/bin/env Rscript
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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3 #####################################################################################################################
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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4 ############## FILTERING RARE AND LOW-ABUNDANCE SPECIES function:filtreEspeceRare ##############################
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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5 #####################################################################################################################
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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7 #### Based on Romain Lorrillière R script
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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8 #### Modified by Alan Amosse and Benjamin Yguel for integrating within Galaxy-E
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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11 suppressMessages(library(reshape2))
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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14 ###########
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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15 #delcaration des arguments et variables/ declaring some variables and load arguments
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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17 args = commandArgs(trailingOnly=TRUE)
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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19 if (length(args)==0) {
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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20 stop("At least one argument must be supplied, dataset transformed by make table function (.tabular).", call.=FALSE) #si pas d'arguments -> affiche erreur et quitte / if no args -> error and exit1
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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21 } else {
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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22 Datatransformedforfiltering_trendanalysis<-args[1] ###### Nom du fichier peut provenir de la fonction "MakeTableAnalyse" / file name , may result from the function "MakeTableAnalys"
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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23 source(args[2])### chargement des fonctions / load the functions
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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24 }
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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26 ##### Le tableau de données doit posséder 3 variables en colonne minimum avec 1 seule espèce et autant de colonne en plus que d'espèces en plus: les carrés ou sont réalisés les observatiosn ("carre"), la ou les années des observations ("annee"), 1 colonne par espèce renseignée avec les abondances correspondantes
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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27 ##### Data must be a dataframe with 3 variables in column: plots where observation where made ("carre"), year(s) of the different sampling ("annee"), and one column per species with its abundance
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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30 #Import des données / Import data
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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31 tab <- read.table(Datatransformedforfiltering_trendanalysis,sep="\t",dec=".",header=TRUE) #
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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33 err_msg_tab="\nThe input dataset doesn't have the right format. It need to have the following 2 variables : \"carre\" and \"annee\" followed by at least one species"
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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34 if(ncol(tab)<3 || !("carre" %in% names(tab)) || !("annee" %in% names(tab))){
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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35 stop(err_msg_tab,call.=FALSE)
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36 }
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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41 #Do your analysis
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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42 tab_filtred1<-filter_absent_species(tab)
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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43 tab_filtred2<-filter_rare_species(tab)
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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45 #save the data in a output file in a tabular format
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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46 filename <- "Datafilteredfortrendanalysis.tabular"
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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47 write.table(tab_filtred2, filename,row.names=FALSE,sep="\t",dec=".")
2e45ae3b297a "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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48 cat(paste("\nWrite table with data filtered for trend analysis. \n--> \"",filename,"\"\n"))
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