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annotate PhyloIndex.R @ 0:88d3f6881490 draft

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author ecology
date Tue, 20 May 2025 09:52:44 +0000
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88d3f6881490 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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1 #!/bin/Rscript
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2 # Indice de phylodiversite
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5 # args
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6 args = commandArgs(trailingOnly=TRUE)
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7 #args = c("comm_matrix", "comm_tree.txt")
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9 # library
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10 library(Matrix)
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11 library(ape)
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12 library(phyloregion)
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13 library(SparseArray)
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15 # functions
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16 write_results <- function(){
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17 write.table(ses_PD, output_file, sep = "\t", row.names=FALSE)
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18 }
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20 # verif args
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21 if (length(args)<5){stop('Usage : input_tree_file input_matrix_file random_seed clustering_model output_file')
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22 }else{
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23 # read enter file
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24 comm_tree <- read.tree(args[1])
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26 comm_matrix <- readSparseCSV(args[2] , sep="\t")
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27 comm_matrix <- as(comm_matrix,"dgCMatrix")
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29 seed <- args[3]
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31 model <- args[4]
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33 output_file <- args[5]
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35 # rdm + compute
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36 set.seed(seed)
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37 ses_PD <- PD_ses(comm_matrix, comm_tree, model = model, reps = 999)
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39 # write res
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40 write_results()
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41 }