[galaxy-user] Tools won't go away even after deleting it from tool_conf.xml

Dear Galaxy users, Has anyone experienced this problem before? In my local instance of Galaxy on a server I've deleted the path of almost all sections with their corresponding tools from tool_conf.xml (wanting to leave my own customized section) but after a restart and a new run of the run.sh there are still two of them (SNP/WGA: Data; Filters and Phenotype Association) left in the tool list with their first tool also appearing. Is there a special setting for those two? Can anyone help me? Thank you, Efthymios Ladoukakis