resolve decontam + citation

multiple taxa manual filtering
issue raised by Olivier Navaud, thx!

R/decontam_fun.R

@@ -294,14 +294,11 @@ decontam_fun <- function(data = data, domain = "Bacteria", output = "./decontam_
     cont_list <- unlist(strsplit(manual_cont,","))
     flog.info(paste('Removing ',cont_list, sep=''))
     ttable = data@tax_table@.Data
-    taxToKeep5=NULL
-    for(i in cont_list){
       if(manual_cont_rank == "ASV"){
-        taxToKeep5 = c(taxToKeep5,row.names(ttable)[row.names(ttable) !=i ]  )
+        taxToKeep5 = !row.names(ttable) %in% cont_list
       }else{
-        taxToKeep5 = c(taxToKeep5,row.names(ttable)[ttable[,manual_cont_rank]!=i])
+        taxToKeep5 = !ttable[,manual_cont_rank] %in% cont_list
       }
-    }
     data <- prune_taxa(taxToKeep5, data)
   }
 

inst/CITATION

+citHeader("To cite ranomaly in publications use:")
+
+citEntry(
+  entry    = "Article",
+  title    = "RANOMALY: AmplicoN WOrkflow for Microbial Community AnaLYsis",
+  author   = "Theil Sebastien and Rifa Etienne",
+  journal  = "F1000Research",
+  year     = "2021",
+  volume   = "10",
+  page     = "7",
+  url      = "https://doi.org/10.12688/f1000research.27268.1",
+  textVersion = paste(
+  "Theil Sebastien, and Rifa Etienne. 2021. « RANOMALY: AmplicoN WOrkflow for Microbial Community AnaLYsis ». F1000Research 10 (january): 7. https://doi.org/10.12688/f1000research.27268.1."
+
+
+  )
+)