GMAP and  GSNAP use added datatypes:

   add datatype definition file: lib/galaxy/datatypes/gmap.py

   add the following import line to:  lib/galaxy/datatypes/registry.py
   import gmap # added for gmap tools

   add to datatypes_conf.xml
        <!-- Start GMAP Datatypes -->
        <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB"  display_in_upload="False"/>
        <!--



Tools:
  GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations
  GMAP - map sequences to a reference sequence GmapDB index
  GSNAP - align sequences to a reference and detect splicing 

  Add to  tool_conf.xml     ( probably in the "NGS: Mapping" section )
   <tool file="gmap/gmap_build.xml" />
   <tool file="gmap/gmap.xml" />
   <tool file="gmap/gsnap.xml" />


TODO:
  Add classes to gmap.py
    IntervalIndexTree  -  datatype for the iit_store result
    IntervalAnnotation  - generic class  for gmap annotation formats
    SpliceSiteAnnotation - class  for gmap splicesite annotation format
    IntronAnnotation - class  for gmap introns  annotation format
    SNPAnnotation - class  for gmap snp  annotation format
    GmapIndex - generic class for a gmap index
    SnpIndex - an index created by  snpindex
    CmetIndex - an index created by cmetindex
    AtoiIndex - an index created by atoiindex

  Possibly add Tools:
    iit_store - creates a mapping index .iit from: gtf,gff3,gmapannotation, UCSC refGene table
    iit_get - retrieves from .iit store 
    get_genome - retrieves from a gmapdb
    snpindex  - create a SNPIndex
    cmetindex - create methylcytosine index
    atoiindex - create  A-to-I RNA editing index