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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
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#!/usr/bin/env Rscript

args = commandArgs(trailingOnly=TRUE)
source(args[1])


tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")})
pheno = read.table(args[3], header=TRUE,sep="	")

if("TREND" %in% colnames(input)){
    input <- input[input$TREND==1,c("SPECIES","SITE","YEAR","MONTH","DAY","COUNT")]
}
data.index <- abundance_index(input, pheno)
write.table(data.index, file="data.index", row.names=FALSE, sep="	")