Mercurial > repos > ecology > eml_validate
diff taxo_cov_template.R @ 0:ad96b20423cf draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
author | ecology |
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date | Fri, 27 Sep 2024 13:01:04 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/taxo_cov_template.R Fri Sep 27 13:01:04 2024 +0000 @@ -0,0 +1,47 @@ +#28/11/2023 +#Seguineau Pauline +#Make taxonomic coverage template + +#Load packages + +library(EMLassemblyline) + +#Load arguments + +args = commandArgs(trailingOnly=TRUE) +if(length(args)>0){ + data_taxa <- args[1] + taxa_table <- args[2] + taxa_col <- as.numeric(args[3]) + taxa_name_type <- args[4] + authority <- as.numeric(args[5]) + authority2 <- as.numeric(args[6]) + authority3 <- as.numeric(args[7]) + empty <- args[8] +} + +#transfom arguments +taxatable = read.table(data_taxa,header=T,sep="\t") +taxacol = names(taxatable[taxa_col]) + +if (authority2 == 0 && authority3==0){ + authority_f = authority} + +if(authority2 == 0 && authority3 != 0){ + authority_f = c(authority,authority3)} + +if (authority2 !=0 && authority3==0){ + authority_f = c(authority,authority2)} + +if (authority3 !=0 && authority2 !=0){ + authority_f = c(authority,authority2,authority3)} + +if (empty == "false"){ + empty = FALSE +}else if (empty=="true"){ + empty=TRUE} + + +#Make template + +template_taxonomic_coverage(path =".", data.path = "data_files", taxa.table = taxa_table, taxa.col = taxacol, taxa.name.type = taxa_name_type , taxa.authority = authority_f, empty = empty)