diff --git a/tools/README.md b/tools/README.md
index 8fce077b40204f4fb6689cd095d7b4d8622cf938..31c15148dfd81ce91b454ec7f1025147505fd2be 100644
--- a/tools/README.md
+++ b/tools/README.md
@@ -18,4 +18,10 @@ All Snakemake tool descriptions try to respect some rules and best practices in
   	* There is usually a `options` to specify all other command line options
   * the shell command
 
-input and output are then set up in the Snakemake file that refer to the rule.
\ No newline at end of file
+input and output are then set up in the Snakemake file that refer to the rule.
+Therefore the rules cannot be used directly.
+
+## Example
+
+The directory for metaphlan2 rules give some example on the way to call the rules as well as setting
+the parameters in the `config.yaml` file.