we're in the process of installing bowtie and bwa to get them working with Galaxy and have a question. Looking at left hand menu item "NGS: Mapping" on the home page of Galaxy that we have just installed we see:

NGS: Mapping
Megablast compare short reads against nt and wgs databases

Digging in tools_config.xml we see:

 <section name="NGS: Mapping" id="solexa_tools">
   <!-- <tool file="sr_mapping/lastz_wrapper.xml" /> -->
   <tool file="metag_tools/megablast_wrapper.xml" />
   <tool file="metag_tools/megablast_xml_parser.xml" />
   <tool file="sr_mapping/bowtie_wrapper.xml" />
   <tool file="sr_mapping/bwa_wrapper.xml" />

Looking in .../tools/sr_mapping we see both:


And checking say bowtie_wrapper.xml we see

<tool id="bowtie_wrapper" name="Bowtie" version="1.0.0">
  <description> fast alignment of reads against reference sequence </description

Everything looks good so why do we not see sub-menu items for bowtie and bwa? All we see under NGS: Mapping are the two items I listed initially, "Megablast compare short reads against nt and wgs databases" and "Parse blast XML output".

Thanks for your help.