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comparison robis.r @ 0:ed3688d04c12 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 13ac67c0a21d742b29e6273cdff058560abad770
author ecology
date Tue, 05 Nov 2024 14:17:28 +0000
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comparison
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-1:000000000000 0:ed3688d04c12
1 #Rscript
2
3 ###########################################
4 ## Retrieve Obis occurences data ##
5 ###########################################
6
7 ##### Packages : robis
8 # https://iobis.github.io/robis/articles/getting-started.html
9 # Get args
10 args <- commandArgs(trailingOnly = TRUE)
11
12 if (length(args) < 1) {
13 stop("This tool needs at least 1 argument : longitude, latitude, species or taxonID")
14 }else {
15 sname <- args[1]
16 taxid <- args[2]
17 lat_min <- args[3]
18 lat_max <- args[4]
19 long_min <- args[5]
20 long_max <- args[6]
21 }
22
23 if (lat_min == "0.0" & lat_max == "0.0" & long_min == "0.0" & long_max == "0.0") {
24 lat_min <- ""
25 lat_max <- ""
26 long_min <- ""
27 long_max <- ""
28 }
29
30 ##### Import data
31 # Get biological occurrences
32 if (lat_min != "" & sname != "" & taxid != "") {
33 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, "))"))
34 }else if (lat_min != "" & sname != "" & taxid == "") {
35 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, "))"))
36 }else if (lat_min != "" & sname == "" & taxid != "") {
37 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, "))"))
38 }else if (lat_min != "" & sname == "" & taxid == "") {
39 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, "))"))
40 }else if (lat_min == "" & sname != "" & taxid != "") {
41 my_occs <- robis::occurrence(scientificname = sname, taxonid = taxid)
42 }else if (lat_min == "" & sname == "" & taxid != "") {
43 my_occs <- robis::occurrence(taxonid = taxid)
44 }else if (lat_min == "" & sname != "" & taxid == "") {
45 my_occs <- robis::occurrence(scientificname = sname)
46 }
47
48
49 # Dispay results
50
51 # If empty
52 if(length(my_occs) == 0) {
53 cat("\nNo occurrences found.\nLittle tip : Check your input typo, some databases are case sensitive : Genus species.\n")
54 }
55
56
57 write.table(file = "output.tab", my_occs, sep = "\t", dec = ".", na = "", row.names = FALSE, col.names = TRUE, quote = FALSE)