update README for tools

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.
+input and output are then set up in the Snakemake file that refer to the rule.
\ No newline at end of file
+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.