Update tools.md - prettier and added a link

doc/tools.md

@@ -76,9 +76,11 @@ source ~/SemEHR/virtenv/bin/activate
 ## Anonymise a directory of text documents
 
 This is optional for the example because there's nothing to anonymise in these documents, but
+```
 export SMI_LOGS_ROOT=.
 export PYTHONPATH=/path/to/Smi_Common_Python # if SmiServices is not yet in your virtualenv
 ./semehr_anon.py -i input_dir -o anon_dir --xml
+```
 
 ## Run SemEHR on the sample document to get the semehr_results
 
@@ -447,6 +449,8 @@ pgCursor.close()
 
 Note: all tables, indexes and functions reside in the `semehr` schema of the `semehr` database.
 
+For full details see the [annotation database document](annotation_database.md)
+
 ## Table: cui_count
 
 The `cui_count` table contains a record of the frequency of each CUI,