Mercurial > repos > ecology > sdmpredictors_list_layers
comparison 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
author | ecology |
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date | Mon, 08 Apr 2024 16:33:11 +0000 |
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-1:000000000000 | 0:f20914d71c9d |
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1 #!/bin/Rscript | |
2 | |
3 args = commandArgs(trailingOnly=TRUE) | |
4 | |
5 #lister les option pour future et paléo, source internet ? | |
6 #donner une erreur quand une option est incorrecte | |
7 | |
8 library(sdmpredictors) | |
9 | |
10 layers_modern_fun <- function(argument_number, file_number){ | |
11 | |
12 data_terrestrial = as.logical(args[argument_number+1]) | |
13 data_marine = as.logical(args[argument_number+2]) | |
14 data_freshwater = as.logical(args[argument_number+3]) | |
15 data_monthly = as.logical(args[argument_number+4]) | |
16 data_version = as.numeric(args[argument_number+5]) | |
17 | |
18 if(data_version==0){data_version <- NULL} | |
19 | |
20 datasets <- list_datasets(terrestrial = data_terrestrial | |
21 , marine = data_marine | |
22 , freshwater = data_freshwater) | |
23 | |
24 write.table(list_layers(datasets | |
25 , terrestrial = data_terrestrial | |
26 , marine = data_marine | |
27 , freshwater = data_freshwater | |
28 , monthly = data_monthly | |
29 , version = data_version | |
30 ), file = paste(as.character(file_number),"data_current.tabular", sep = "_"), sep = "\t", row.names=FALSE) | |
31 } | |
32 | |
33 layers_future_fun <- function(argument_number, file_number){ | |
34 | |
35 data_terrestrial = as.logical(args[argument_number+1]) | |
36 data_marine = as.logical(args[argument_number+2]) | |
37 data_freshwater = as.logical(args[argument_number+3]) | |
38 data_monthly = as.logical(args[argument_number+4]) | |
39 data_version = as.numeric(args[argument_number+5]) | |
40 data_scenario = as.character(args[argument_number+6]) | |
41 data_year = as.numeric(args[argument_number+7]) | |
42 | |
43 if(data_version==0){data_version <- NULL} | |
44 if(data_scenario=="All"){data_scenario <- NA} | |
45 if(data_year==0){data_year <- NA} | |
46 | |
47 datasets <- list_datasets(terrestrial = data_terrestrial | |
48 , marine = data_marine | |
49 , freshwater = data_freshwater) | |
50 | |
51 write.table(list_layers_future(datasets | |
52 , terrestrial = data_terrestrial | |
53 , marine = data_marine | |
54 , freshwater = data_freshwater | |
55 , monthly = data_monthly | |
56 , version = data_version | |
57 , scenario = data_scenario | |
58 , year = data_year | |
59 ), file = paste(as.character(file_number),"data_future.tabular", sep = "_"), sep = "\t", row.names=FALSE) | |
60 } | |
61 | |
62 layers_paleo_fun <- function(argument_number, file_number){ | |
63 | |
64 data_terrestrial = as.logical(args[argument_number+1]) | |
65 data_marine = as.logical(args[argument_number+2]) | |
66 data_freshwater = as.logical(args[argument_number+3]) | |
67 data_monthly = as.logical(args[argument_number+4]) | |
68 data_version = as.numeric(args[argument_number+5]) | |
69 data_model_name = as.character(args[argument_number+6]) | |
70 data_epoch = as.character(args[argument_number+7]) | |
71 data_years_ago = as.numeric(args[argument_number+8]) | |
72 | |
73 if(data_version==0){data_versio <- NULL} | |
74 if(data_model_name=="All"){data_model_name <- NA} | |
75 if(data_epoch=="All"){data_epoch <- NA} | |
76 if(data_years_ago==0){data_years_ago <- NA} | |
77 | |
78 datasets <- list_datasets(terrestrial = data_terrestrial | |
79 , marine = data_marine | |
80 , freshwater = data_freshwater) | |
81 | |
82 write.table(list_layers_paleo(datasets | |
83 , terrestrial = data_terrestrial | |
84 , marine = data_marine | |
85 , freshwater = data_freshwater | |
86 , monthly = data_monthly | |
87 , version = data_versio | |
88 , model_name = data_model_name | |
89 , epoch = data_epoch | |
90 , years_ago = data_years_ago | |
91 ), file = paste(as.character(file_number),"data_paleo.tabular", sep = "_"), sep = "\t", row.names=FALSE) | |
92 } | |
93 | |
94 | |
95 if (length(args)<0){stop("not enough arguments") | |
96 }else{ | |
97 n <- 1 | |
98 for (a in 1:length(args)) { | |
99 if (as.character(args[a]) == "layers_current"){ | |
100 layers_modern_fun(a,n) | |
101 n <- n+1 | |
102 } | |
103 | |
104 if (as.character(args[a]) == "layers_future"){ | |
105 layers_future_fun(a,n) | |
106 n <- n+1 | |
107 } | |
108 | |
109 if (as.character(args[a]) == "layers_paleo"){ | |
110 layers_paleo_fun(a,n) | |
111 n <- n+1 | |
112 } | |
113 }} | |
114 | |
115 | |
116 | |
117 | |
118 | |
119 |