diff sdmpredictors_list_layers.R @ 0:f20914d71c9d draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sdmpredictors_list_layers.R	Mon Apr 08 16:33:11 2024 +0000
@@ -0,0 +1,119 @@
+#!/bin/Rscript
+
+args = commandArgs(trailingOnly=TRUE)
+
+#lister les option pour future et paléo, source internet ?
+#donner une erreur quand une option est incorrecte
+
+library(sdmpredictors)
+
+layers_modern_fun <- function(argument_number, file_number){
+  
+  data_terrestrial = as.logical(args[argument_number+1])
+  data_marine      = as.logical(args[argument_number+2])
+  data_freshwater  = as.logical(args[argument_number+3])
+  data_monthly     = as.logical(args[argument_number+4])
+  data_version     = as.numeric(args[argument_number+5])
+  
+  if(data_version==0){data_version <- NULL}
+  
+  datasets <- list_datasets(terrestrial = data_terrestrial
+                            , marine = data_marine
+                            , freshwater = data_freshwater)
+  
+  write.table(list_layers(datasets
+                         , terrestrial = data_terrestrial
+                         , marine = data_marine
+                         , freshwater = data_freshwater
+                         , monthly = data_monthly
+                         , version = data_version
+                         ), file = paste(as.character(file_number),"data_current.tabular", sep = "_"), sep = "\t", row.names=FALSE)
+}
+
+layers_future_fun <- function(argument_number, file_number){
+  
+  data_terrestrial = as.logical(args[argument_number+1])
+  data_marine      = as.logical(args[argument_number+2])
+  data_freshwater  = as.logical(args[argument_number+3])
+  data_monthly     = as.logical(args[argument_number+4])
+  data_version     = as.numeric(args[argument_number+5])
+  data_scenario    = as.character(args[argument_number+6])
+  data_year        = as.numeric(args[argument_number+7])
+  
+  if(data_version==0){data_version <- NULL}
+  if(data_scenario=="All"){data_scenario <- NA}
+  if(data_year==0){data_year <- NA}
+  
+  datasets <- list_datasets(terrestrial = data_terrestrial
+                            , marine = data_marine
+                            , freshwater = data_freshwater)
+                            
+  write.table(list_layers_future(datasets
+                                , terrestrial = data_terrestrial
+                                , marine = data_marine
+                                , freshwater = data_freshwater
+                                , monthly = data_monthly
+                                , version = data_version
+                                , scenario = data_scenario
+                                , year = data_year
+                                ), file = paste(as.character(file_number),"data_future.tabular", sep = "_"), sep = "\t", row.names=FALSE)
+}
+
+layers_paleo_fun <- function(argument_number, file_number){
+  
+  data_terrestrial = as.logical(args[argument_number+1])
+  data_marine      = as.logical(args[argument_number+2])
+  data_freshwater  = as.logical(args[argument_number+3])
+  data_monthly     = as.logical(args[argument_number+4])
+  data_version     = as.numeric(args[argument_number+5])
+  data_model_name  = as.character(args[argument_number+6])
+  data_epoch       = as.character(args[argument_number+7])
+  data_years_ago   = as.numeric(args[argument_number+8])
+  
+  if(data_version==0){data_versio <- NULL}
+  if(data_model_name=="All"){data_model_name <- NA}
+  if(data_epoch=="All"){data_epoch <- NA}
+  if(data_years_ago==0){data_years_ago <- NA}
+  
+  datasets <- list_datasets(terrestrial = data_terrestrial
+                            , marine = data_marine
+                            , freshwater = data_freshwater)
+                            
+  write.table(list_layers_paleo(datasets
+                                , terrestrial = data_terrestrial
+                                , marine = data_marine
+                                , freshwater = data_freshwater
+                                , monthly = data_monthly
+                                , version = data_versio
+                                , model_name = data_model_name
+                                , epoch = data_epoch 
+                                , years_ago = data_years_ago
+                                ), file = paste(as.character(file_number),"data_paleo.tabular", sep = "_"), sep = "\t", row.names=FALSE)
+}
+
+
+if (length(args)<0){stop("not enough arguments")
+}else{
+  n <- 1
+  for (a in 1:length(args)) {
+    if (as.character(args[a]) == "layers_current"){
+      layers_modern_fun(a,n)
+      n <- n+1
+    }
+
+    if (as.character(args[a]) == "layers_future"){
+      layers_future_fun(a,n)
+      n <- n+1
+    }
+  
+    if (as.character(args[a]) == "layers_paleo"){
+      layers_paleo_fun(a,n)
+      n <- n+1
+    }
+}}
+
+
+
+
+
+