| Previous changeset 1:edb8d19735a6 (2024-01-24) Next changeset 3:844b5bf84164 (2024-09-11) |
|
Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e |
|
modified:
cluster.xml recup_liste_taxon.R test-data/ceamarc_env.tsv |
|
added:
GeoNN.R test-data/fish_wide.tsv |
| b |
| diff -r edb8d19735a6 -r 24a81631a8b5 GeoNN.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GeoNN.R Thu Mar 21 14:04:36 2024 +0000 |
| [ |
| @@ -0,0 +1,77 @@ +#Date : 09/02/2024 +#Author : Seguineau Pauline + +#Load libraries +library(tidyr) +library(dplyr) +library(sf) + +#load arguments +args = commandArgs(trailingOnly=TRUE) +if (length(args)==0) +{ + stop("This tool needs at least one argument") +}else{ + enviro <- args[1] + envlong <- as.numeric(args[2]) + envlat <- as.numeric(args[3]) + occu <- args[4] + occulat <- as.numeric(args[5]) + occulong <- as.numeric(args[6]) +} + +env = read.table(enviro, header = TRUE, sep="\t") +occ = read.table(occu, header = TRUE, sep = "\t") + +cols_env = c(names(env[envlong]),names(env[envlat])) +cols_occ = c(names(occ[occulong]),names(occ[occulat])) + +###calculate distances### +#transform tables into sf object + +env_sf <- st_as_sf(env, coords = cols_env, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs") +occ_sf <- st_as_sf(occ, coords = cols_occ, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs") + +#Find the indices of env_sf entities closest to each point in occ_sf. + +nearest_indices <- st_nearest_feature(occ_sf, env_sf) + +nearest_points <- env[nearest_indices, ] + +# Calculate distances between env_sf and occ_sf points +distances <- st_distance(env_sf, occ_sf) + +#Extract the corresponding distances between occ and env + +nearest_distances <- numeric(length(nearest_indices)) + +for (i in 1:length(nearest_indices)) { + nearest_distances[i] <- st_distance(env_sf[nearest_indices[i],], occ_sf[i,]) +} + +#assemble occurrences and environmental parameters in the same file + +nearest_points <- nearest_points[, !names(nearest_points) %in% cols_env] #remove lat and long from env to clean data +new_occ = cbind(occ, nearest_points) + +#Save the file + +write.table(new_occ, file = "occurrence_env.tsv",sep ="\t",quote = F, row.names = F,col.names = T) + +#create an information file with the distances between the points of the two files + +distance_info <- data.frame( + occ_geometry = occ_sf$geometry, + env_geometry = env_sf$geometry[nearest_indices], + distance = nearest_distances +) + +colnames(distance_info)[1] <- "occ_geometry" +colnames(distance_info)[2] <- "env_geometry" +colnames(distance_info)[3] <- "Distances (meters)" +#save the information file + +write.table(distance_info, file = "infos_file.tsv",sep ="\t",quote = F, row.names = F,col.names = T) + + + |
| b |
| diff -r edb8d19735a6 -r 24a81631a8b5 cluster.xml --- a/cluster.xml Wed Jan 24 15:53:07 2024 +0000 +++ b/cluster.xml Thu Mar 21 14:04:36 2024 +0000 |
| b |
| @@ -22,7 +22,7 @@ <inputs> <param name="envfile" type="data" format="tabular" label="Environmental file (tabular only)"/> <param name="predictionmatrix" type="data" format="tabular" label="Prediction matrix (file 'data to cluster' from Cluster Estimate tool)"/> - <param name="predictionfile" type="data" format="tabular" label="Prediction file (file 'data.bio table' from Cluster Estimate tool)"/> + <param name="predictionfile" type="data" format="tabular" label="Prediction table (file 'data.bio table' from Cluster Estimate tool)"/> <param name="k" type="integer" label="Number of Cluster wanted" min= "1" value="2"/> <param name="metric" type="select" label="What metric to use to calculate dissimilarities between observations ?"> <option value = "manhattan">manhattan</option> @@ -46,7 +46,7 @@ <param name='sample' value="10"/> <output name='output1'> <assert_contents> - <has_size value="7369" delta="1000"/> + <has_size value="8359" delta="500"/> </assert_contents> </output> <output name='output2'> |
| b |
| diff -r edb8d19735a6 -r 24a81631a8b5 recup_liste_taxon.R --- a/recup_liste_taxon.R Wed Jan 24 15:53:07 2024 +0000 +++ b/recup_liste_taxon.R Thu Mar 21 14:04:36 2024 +0000 |
| b |
| @@ -82,7 +82,7 @@ #extraction of the have_model object write.table(have_model,file = "have_model.tsv", sep="\t", quote = F, row.names = F) -#getting list of taxa for next if not using worms +#getting list of taxa for next step if not using worms list_taxon = have_model3$Taxa write.table(list_taxon, file= "list_taxa.txt", quote = F, row.names = F, col.names = F) |
| b |
| diff -r edb8d19735a6 -r 24a81631a8b5 test-data/ceamarc_env.tsv --- a/test-data/ceamarc_env.tsv Wed Jan 24 15:53:07 2024 +0000 +++ b/test-data/ceamarc_env.tsv Thu Mar 21 14:04:36 2024 +0000 |
| b |
| @@ -1,16 +1,16 @@ -long lat Carbo Grav Maxbearing Maxmagnit Meancurmag Meansal Meantheta Mud Prof Rugosity Sand Seaice_prod Sili Slope Standcurmag Standsal Standtheta long_round lat_round -1 139.22 -65.57 0.88 28.59 3.67 0.03 0.03 34.62 -0.13 22.72 -441 -9999 55.76 0.24 3.27 0.28 0.01 0.01 0.18 139,22 -65,57 -2 139.22 -65.57 0.88 28.61 3.64 0.02 0.03 34.62 -0.13 22.48 -439 -9999 55.74 0.24 3.29 0.27 0.01 0.01 0.18 139,22 -65,57 -3 139.23 -65.57 0.92 28.62 3.59 0.02 0.03 34.62 -0.14 22.25 -438 -9999 56.28 0.25 3.32 0.22 0.01 0.01 0.19 139,23 -65,57 -4 139.24 -65.57 0.92 28.63 3.51 0.01 0.03 34.62 -0.14 21.95 -436 -9999 56.57 0.26 3.3 0.08 0.01 0.01 0.19 139,24 -65,57 -5 139.24 -65.57 0.92 28.64 3.35 0.01 0.03 34.62 -0.14 21.7 -437 -9999 56.58 0.26 3.28 0.05 0.01 0.01 0.19 139,24 -65,57 -6 139.25 -65.57 0.93 28.65 3 0.0096293305978179 0.03 34.62 -0.15 21.44 -436 -9999 56.63 0.26 3.26 0.29 0.01 0.01 0.19 139,25 -65,57 -7 139.26 -65.57 0.93 28.63 2.49 0.00871255807578564 0.03 34.62 -0.15 21.11 -432 -9999 56.67 0.26 3.23 0.43 0.01 0.01 0.19 139,26 -65,57 -8 139.26 -65.57 0.93 28.64 2.01 0.01 0.03 34.62 -0.16 20.83 -429 -9999 56.71 0.26 3.21 0.37 0.01 0.01 0.19 139,26 -65,57 -9 139.27 -65.57 0.94 28.65 1.71 0.01 0.03 34.62 -0.16 20.55 -427 -9999 56.75 0.26 3.19 0.32 0.01 0.01 0.2 139,27 -65,57 -10 139.28 -65.57 0.94 28.66 1.54 0.01 0.03 34.62 -0.16 20.21 -424 -9999 56.8 0.26 3.17 0.28 0.01 0.01 0.2 139,28 -65,57 -11 139.28 -65.57 0.94 28.67 1.44 0.02 0.03 34.62 -0.17 19.74 -422 -9999 56.84 0.26 3.14 0.26 0.01 0.01 0.2 139,28 -65,57 -12 139.29 -65.57 0.94 28.68 1.74 0.01 0.03 34.62 -0.17 20.86 -421 -9999 56.87 0.26 3.13 0.22 0.01 0.01 0.2 139,29 -65,57 -13 139.3 -65.57 0.95 28.7 3.46 0.01 0.03 34.62 -0.17 21.3 -420 -9999 56.91 0.26 3.11 0.32 0.01 0.01 0.2 139,30 -65,57 -14 139.3 -65.57 0.95 28.71 3.91 0.03 0.03 34.62 -0.18 21.01 -414 -9999 57.18 0.26 3.09 0.59 0.01 0.01 0.21 139,30 -65,57 -15 139.31 -65.57 0.96 28.72 4.03 0.05 0.03 34.62 -0.18 20.76 -406 -9999 57.54 0.26 3.07 0.53 0.01 0.01 0.21 139,31 -65,57 +long lat Carbo Grav Maxbearing Maxmagnit Meancurmag Meansal Meantheta Mud Prof Rugosity Sand Seaice_prod Sili Slope Standcurmag Standsal Standtheta +139.22 -65.57 0.88 28.59 3.67 0.03 0.03 34.62 -0.13 22.72 -441 -9999 55.76 0.24 3.27 0.28 0.01 0.01 0.18 +139.22 -65.57 0.88 28.61 3.64 0.02 0.03 34.62 -0.13 22.48 -439 -9999 55.74 0.24 3.29 0.27 0.01 0.01 0.18 +139.23 -65.57 0.92 28.62 3.59 0.02 0.03 34.62 -0.14 22.25 -438 -9999 56.28 0.25 3.32 0.22 0.01 0.01 0.19 +139.24 -65.57 0.92 28.63 3.51 0.01 0.03 34.62 -0.14 21.95 -436 -9999 56.57 0.26 3.3 0.08 0.01 0.01 0.19 +139.24 -65.57 0.92 28.64 3.35 0.01 0.03 34.62 -0.14 21.7 -437 -9999 56.58 0.26 3.28 0.05 0.01 0.01 0.19 +139.25 -65.57 0.93 28.65 3 0.0096293305978179 0.03 34.62 -0.15 21.44 -436 -9999 56.63 0.26 3.26 0.29 0.01 0.01 0.19 +139.26 -65.57 0.93 28.63 2.49 0.00871255807578564 0.03 34.62 -0.15 21.11 -432 -9999 56.67 0.26 3.23 0.43 0.01 0.01 0.19 +139.26 -65.57 0.93 28.64 2.01 0.01 0.03 34.62 -0.16 20.83 -429 -9999 56.71 0.26 3.21 0.37 0.01 0.01 0.19 +139.27 -65.57 0.94 28.65 1.71 0.01 0.03 34.62 -0.16 20.55 -427 -9999 56.75 0.26 3.19 0.32 0.01 0.01 0.2 +139.28 -65.57 0.94 28.66 1.54 0.01 0.03 34.62 -0.16 20.21 -424 -9999 56.8 0.26 3.17 0.28 0.01 0.01 0.2 +139.28 -65.57 0.94 28.67 1.44 0.02 0.03 34.62 -0.17 19.74 -422 -9999 56.84 0.26 3.14 0.26 0.01 0.01 0.2 +139.29 -65.57 0.94 28.68 1.74 0.01 0.03 34.62 -0.17 20.86 -421 -9999 56.87 0.26 3.13 0.22 0.01 0.01 0.2 +139.3 -65.57 0.95 28.7 3.46 0.01 0.03 34.62 -0.17 21.3 -420 -9999 56.91 0.26 3.11 0.32 0.01 0.01 0.2 +139.3 -65.57 0.95 28.71 3.91 0.03 0.03 34.62 -0.18 21.01 -414 -9999 57.18 0.26 3.09 0.59 0.01 0.01 0.21 +139.31 -65.57 0.96 28.72 4.03 0.05 0.03 34.62 -0.18 20.76 -406 -9999 57.54 0.26 3.07 0.53 0.01 0.01 0.21 |
| b |
| diff -r edb8d19735a6 -r 24a81631a8b5 test-data/fish_wide.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fish_wide.tsv Thu Mar 21 14:04:36 2024 +0000 |
| b |
| @@ -0,0 +1,20 @@ +lat long rajidae_bathyraja_sp. myctophidae_electrona_antarctica myctophidae_protomyctophum_bolini +-67.22 139.96 4 1 0 +-65.46 139.31 0 4 0 +-65.82 142.96 0 0 1 +-65.77 142.92 0 1 1 +-65.64 140.45 0 2 0 +-65.74 142.86 0 1 0 +-65.85 144.04 0 2 0 +-65.44 139.32 0 0 0 +-65.71 140.6 0 0 0 +-66.75 143.95 0 0 0 +-66.41 140.51 0 0 0 +-66.34 140.03 0 0 0 +-66.17 139.35 0 0 0 +-66.33 143.36 0 0 0 +-66.39 140.43 0 0 0 +-66.75 144.96 0 0 0 +-66.34 143.04 0 0 0 +-67.05 145.15 0 0 0 + |