Mercurial > repos > ecology > regionalgam_glmmpql
diff flight-curve.R @ 0:f3e1b6d244a6 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
| author | ecology |
|---|---|
| date | Thu, 20 Jun 2019 04:03:57 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flight-curve.R Thu Jun 20 04:03:57 2019 -0400 @@ -0,0 +1,8 @@ +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) +source(args[1]) #TODO replace by library(regionalGAM) if available as official package from bioconda +tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")}) +dataset1 <- input[,c("SPECIES", "SITE", "YEAR", "MONTH", "DAY", "COUNT")] +pheno <- flight_curve(dataset1, MinVisit = args[3], MinOccur = args[4]) + +write.table(pheno, file="pheno", row.names=FALSE, sep=" ")