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view geo_cov_temp.R @ 1:6de4b4f70b7b draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
author ecology
date Sat, 23 Dec 2023 20:39:13 +0000
parents 8631291a1527
children 32707c9f5261
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#27/11/2023
#Seguineau Pauline
#Make geographic coverage template

#Load packages

library(EMLassemblyline)

#Load arguments

args = commandArgs(trailingOnly=TRUE)
if(length(args)>0){
  
  data_table <- args[1]
  tablename <- args[2]
  lat_col <- as.numeric(args[3])
  long_col <- as.numeric(args[4])
  site_col <- as.numeric(args[5])
  empty <- args[6]
}

datatable = read.table(data_table,header=T)

latcol = names(datatable[lat_col])
longcol = names(datatable[long_col])
sitecol = names(datatable[site_col])

if (empty == "false"){
   empty = FALSE
}else if (empty=="true"){
   empty=TRUE}


#Make template

template_geographic_coverage(path =".", data.path = "data_files", data.table = tablename, lat.col = latcol, lon.col = longcol, site.col = sitecol, empty = empty)