diff taxo_cov_template.R @ 0:fab3ca90cb26 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/taxo_cov_template.R	Tue Sep 10 12:53:05 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)