| Previous changeset 6:14bad9452425 (2025-05-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927 |
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added:
indval.R test-data/Cluster_points.tabular test-data/Merged_table.tabular |
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| diff -r 14bad9452425 -r cec1f7495897 indval.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/indval.R Wed Jul 23 14:36:49 2025 +0000 |
| [ |
| @@ -0,0 +1,59 @@ +#Seguineau Pauline +#02/12/2024 +#Indicspecies tool + +library(dplyr) +library(indicspecies) + +#load arguments +args = commandArgs(trailingOnly=TRUE) +if (length(args)==0) +{ + stop("This tool needs at least one argument") +}else{ + clus_pts <- args[1] + occ <- args[2] + spe_name <- args[3] + sign <- args[4] +} + +###load data +clus <- read.table(clus_pts, dec=".", sep="\t", header=T,na.strings = "na") #cluster points file (ecoregionalization workflow) +data.col <- read.table(occ, dec=".", sep="\t", header=T,na.strings = "na") #occurrence file (merged table from ecoregionalization workflow) +spe_name = strsplit(spe_name, ",") +spname=NULL + +for (n in spe_name) { +spname = cbind(names(data.col[as.numeric(n)]))} + +#Rename decimalLatitude and decimalLongitude columns from occurrence file +if ("decimalLatitude" %in% colnames(data.col)) { + colnames(data.col)[which(colnames(data.col) == "decimalLatitude")] <- "lat" +} +if ("decimalLongitude" %in% colnames(data.col)) { + colnames(data.col)[which(colnames(data.col) == "decimalLongitude")] <- "long" +} + +#Round lat and long of the data.col file to be able to put clus cluster in it +data.col$lat = round(data.col$lat,digits = 2) +data.col$long = round(data.col$long,digits = 2) + +# Creates a new "station" column that associates a unique identifier to each latitude-longitude pair +data.col <- data.col %>% mutate(station = as.factor(paste(lat, long, sep = "_"))) + +# convert "station" to a unique numeric identifier +data.col <- data.col %>% mutate(station = as.numeric(factor(station))) + +#Adding clusters to file +clusta <- merge(data.col,clus, by=c("lat","long"), all.x = TRUE) + +#This generated duplicates with different clusters +clusta <- aggregate(clusta, by=list(clusta$station,clusta$cluster), FUN=mean, na.rm=TRUE) +clusta <- na.exclude(clusta) + +# indval on all clusters +indval = multipatt(clusta[,spname], clusta$cluster,duleg = TRUE, control = how(nperm=999)) +if (sign=="true"){ + capture.output(summary(indval,indvalcomp=TRUE), file = "indval.txt") +}else{ + capture.output(summary(indval,indvalcomp=TRUE, alpha=1), file = "indval.txt")} |
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| diff -r 14bad9452425 -r cec1f7495897 test-data/Cluster_points.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Cluster_points.tabular Wed Jul 23 14:36:49 2025 +0000 |
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| b'@@ -0,0 +1,62195 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| diff -r 14bad9452425 -r cec1f7495897 test-data/Merged_table.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Merged_table.tabular Wed Jul 23 14:36:49 2025 +0000 |
| b |
| b'@@ -0,0 +1,81 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|