Mercurial > repos > ecology > regionalgam_flight_curve

annotate flight-curve.R @ 0:fff507f00b2b draft default tip

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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 04:03:07 -0400
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fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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1 #!/usr/bin/env Rscript
fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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2 args = commandArgs(trailingOnly=TRUE)
fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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3 source(args[1]) #TODO replace by library(regionalGAM) if available as official package from bioconda
fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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4 tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")})
fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
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5 dataset1 <- input[,c("SPECIES", "SITE", "YEAR", "MONTH", "DAY", "COUNT")]
fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
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6 pheno <- flight_curve(dataset1, MinVisit = args[3], MinOccur = args[4])
fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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7
fff507f00b2b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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8 write.table(pheno, file="pheno", row.names=FALSE, sep=" ")