user output for R script

really it's for debugging....
roblanf · Aug 17, 2020 · a42b42a · a42b42a
1 parent 52d0a13
commit a42b42a
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/scripts/clean_tree.R b/scripts/clean_tree.R
@@ -1,12 +1,18 @@
 #!/usr/bin/env Rscript
 
-# usage: Rscript clean_tree.R input_tree input_alignment
+# usage: Rscript clean_tree.R input_tree names_of_species_in_alignment.txt
+# the names file should be one name per line
 
 args = commandArgs(trailingOnly=TRUE)
 
 library(ape)
 library(readr)
 
+print("Input tree")
+print(t)
+print("input names")
+print(a)
+
 
 t = read.tree(args[1])
 a = scan(args[2])