diff robis.r @ 4:393957ecc97d draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/robis.r	Thu Jan 18 09:34:02 2024 +0000
@@ -0,0 +1,57 @@
+#Rscript
+
+###########################################
+##     Retrieve Obis occurences data     ##
+###########################################
+
+##### Packages : robis
+# https://iobis.github.io/robis/articles/getting-started.html
+# Get args
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args) < 1) {
+    stop("This tool needs at least 1 argument : longitude, latitude, species or taxonID")
+}else {
+    sname <- args[1]
+    taxid <- args[2]
+    lat_min <- args[3]
+    lat_max <- args[4]
+    long_min <- args[5]
+    long_max <- args[6]
+}
+
+if (lat_min == "0.0" & lat_max == "0.0" & long_min == "0.0" & long_max == "0.0") {
+lat_min <- ""
+lat_max <- ""
+long_min <- ""
+long_max <- ""
+}
+
+##### Import data
+# Get biological occurrences
+if (lat_min != "" & sname != "" & taxid != "") {
+my_occs <- robis::occurrence(scientificname = sname, taxonid = taxid, geometry = paste("POLYGON ((", long_min, lat_min,  ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))"))
+}else if (lat_min != "" & sname != "" & taxid == "") {
+my_occs <- robis::occurrence(scientificname = sname, geometry = paste("POLYGON ((", long_min, lat_min,  ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))"))
+}else if (lat_min != "" & sname == "" & taxid != "") {
+my_occs <- robis::occurrence(taxonid = taxid, geometry = paste("POLYGON ((", long_min, lat_min,  ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))"))
+}else if (lat_min != "" & sname == "" & taxid == "") {
+my_occs <- robis::occurrence(geometry = paste("POLYGON ((", long_min, lat_min,  ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))"))
+}else if (lat_min == "" & sname != "" & taxid != "") {
+my_occs <- robis::occurrence(scientificname = sname, taxonid = taxid)
+}else if (lat_min == "" & sname == "" & taxid != "") {
+my_occs <- robis::occurrence(taxonid = taxid)
+}else if (lat_min == "" & sname != "" & taxid == "") {
+my_occs <- robis::occurrence(scientificname = sname)
+}
+
+
+# Dispay results
+
+# If empty
+if(length(my_occs) == 0) {
+cat("\nNo occurrences found.\nLittle tip : Check your input typo, some databases are case sensitive : Genus species.\n")
+}
+
+
+write.table(file = "output.tab", my_occs, sep = "\t", dec = ".", na = "", row.names = FALSE, col.names = TRUE, quote = FALSE)