# HG changeset patch
# User ecology
# Date 1747734728 0
# Node ID d19c3cbbdd7ed59af328ea8f755f17d16c0dc3b8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
diff -r 000000000000 -r d19c3cbbdd7e CRSconverter.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CRSconverter.R Tue May 20 09:52:08 2025 +0000
@@ -0,0 +1,84 @@
+#!/bin/Rscript
+# GRID CREATION
+args = commandArgs(trailingOnly=TRUE)
+
+library(sf)
+library(tidyr)
+
+
+save_as_pdf_fun <- function(){
+
+ pdf(file = "output.pdf")
+ plot(st_geometry(Transformed_spacial_coordinates))
+ dev.off()
+}
+
+
+save_as_image_fun <- function(format){
+
+ filename <- paste0("output.", format)
+ # Ouvre le bon device graphique selon le format demandé
+ switch(format,
+ png = png(filename),
+ jpeg = jpeg(filename),
+ tiff = tiff(filename),
+ bmp = bmp(filename),
+ stop("Unsupported format: ", format)
+ )
+ plot(st_geometry(Transformed_spacial_coordinates))
+ dev.off()
+}
+
+
+save_as_shp_fun <- function(){
+ write_sf(Transformed_spacial_coordinates, "output.shp")
+}
+
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+if (length(args)<1){stop('please provide spacial coordinates files(.shp files)')
+}else{
+ Spacial_coordinates_files <- read_sf(as.character(args[1]), layer = 'shapefile')
+ output_file <- args[10]
+
+ projection <- paste('+proj='
+ , as.character(args[2])
+ , ' +lat_0='
+ , as.character(args[3])
+ , ' +lon_0='
+ , as.character(args[4])
+ , ' +x_0='
+ , as.character(args[5])
+ , ' +y_0='
+ , as.character(args[6])
+ , ' +ellps='
+ , as.character(args[7])
+ , ' +datum='
+ , as.character(args[7])
+ , ' +units='
+ , as.character(args[8])
+ , ' +no_defs', sep = "", collapse = NULL) #presonalisation du systeme de références
+
+ Transformed_spacial_coordinates <- st_transform(Spacial_coordinates_files, crs = projection)
+
+ if (as.character(args[9]) == "pdf") {
+ save_as_pdf_fun()
+
+ } else if (as.character(args[9]) == "shp") {
+ save_as_shp_fun()
+
+ } else {
+ save_as_image_fun(as.character(args[9]))
+ }
+}
+
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+#write.table(Transformed_spacial_coordinates, file = "output.tabular", sep="\t", row.names=FALSE)
+ #enregistrement dans quoi ?
+
+#this tool convert shp files to the right format for whatever you like ~a phylodiversity analysis
diff -r 000000000000 -r d19c3cbbdd7e CRSconverter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CRSconverter.xml Tue May 20 09:52:08 2025 +0000
@@ -0,0 +1,250 @@
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+ from environmental predictors for species distribution modeling
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+ 1.0
+ 0
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+ r-sf
+ r-tidyr
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+ output_file_format != 'shp'
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+ output_file_format == 'shp'
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+ 10.32614/CRAN.package.sf
+ 10.32614/CRAN.package.tidyr
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diff -r 000000000000 -r d19c3cbbdd7e test-data/composite_dataset/composite_dataset_shp.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/composite_dataset/composite_dataset_shp.html Tue May 20 09:52:08 2025 +0000
@@ -0,0 +1,17 @@
+Shapefile Galaxy Composite Dataset
+This composite dataset is composed of the following files:
This composite dataset is composed of the following files: