diff geo_cov_temp.R @ 0:fab3ca90cb26 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/geo_cov_temp.R	Tue Sep 10 12:53:05 2024 +0000
@@ -0,0 +1,38 @@
+#27/11/2023
+#Seguineau Pauline
+#Make geographic coverage template
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+  
+  data_table <- args[1]
+  tablename <- args[2]
+  lat_col <- as.numeric(args[3])
+  long_col <- as.numeric(args[4])
+  site_col <- as.numeric(args[5])
+  empty <- args[6]
+}
+
+datatable = read.table(data_table,sep="\t",header=T)
+
+latcol = names(datatable[lat_col])
+longcol = names(datatable[long_col])
+sitecol = names(datatable[site_col])
+
+if (empty == "false"){
+   empty = FALSE
+}else if (empty=="true"){
+   empty=TRUE}
+
+
+#Make template
+
+template_geographic_coverage(path =".", data.path = "data_files", data.table = tablename, lat.col = latcol, lon.col = longcol, site.col = sitecol, empty = empty)
+
+