diff PhyloIndex.R @ 0:71a46f890035 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PhyloIndex.R	Tue May 20 09:53:58 2025 +0000
@@ -0,0 +1,41 @@
+#!/bin/Rscript
+# Indice de phylodiversite
+
+
+# args 
+args = commandArgs(trailingOnly=TRUE)
+#args = c("comm_matrix", "comm_tree.txt")
+
+# library
+library(Matrix)
+library(ape)
+library(phyloregion)
+library(SparseArray)
+
+# functions
+write_results <- function(){
+  write.table(ses_PD, output_file, sep = "\t", row.names=FALSE)
+}
+
+# verif args
+if (length(args)<5){stop('Usage : input_tree_file input_matrix_file random_seed clustering_model output_file')
+}else{
+  # read enter file
+  comm_tree <- read.tree(args[1])
+
+  comm_matrix <- readSparseCSV(args[2] , sep="\t")
+  comm_matrix <- as(comm_matrix,"dgCMatrix")
+
+  seed <- args[3]
+
+  model <- args[4]
+
+  output_file <- args[5]
+
+  # rdm + compute
+  set.seed(seed)
+  ses_PD <- PD_ses(comm_matrix, comm_tree, model = model, reps = 999)
+  
+  # write res 
+  write_results()
+}