add vel datatype,register and example

config/datatypes_conf.xml.sample

@@ -575,6 +575,7 @@
     <datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true"/>
     <datatype extension="dcd" type="galaxy.datatypes.binary:Dcd" display_in_upload="true"/>
+    <datatype extension="vel" type="galaxy.datatypes.binary:Vel" display_in_upload="true"/>
     <datatype extension="grd" type="galaxy.datatypes.molecules:grd" display_in_upload="true"/>
     <datatype extension="grd.tgz" type="galaxy.datatypes.molecules:grdtgz" display_in_upload="true"/>
     <!-- mothur formats -->
@@ -727,6 +728,7 @@
     <sniffer type="galaxy.datatypes.binary:Idat"/>
     <sniffer type="galaxy.datatypes.binary:Trr"/>
     <sniffer type="galaxy.datatypes.binary:Dcd"/>
+    <sniffer type="galaxy.datatypes.binary:Vel"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>

lib/galaxy/datatypes/binary.py

@@ -1959,6 +1959,58 @@ class Dcd(Binary):
             return "Binary CHARMM/NAMD dcd file (%s)" % (nice_size(dataset.get_size()))
 
 
+class Vel(Binary):
+    """
+    Class describing a velocity file from the CHARMM molecular simulation program
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test_charmm.vel')
+    >>> Vel().sniff(fname)
+    True
+    >>> fname = get_test_fname('interval.interval')
+    >>> Vel().sniff(fname)
+    False
+    """
+    file_ext = "vel"
+    edam_format = "format_3842"  # molecular simulation data
+
+    def __init__(self, **kwd):
+        Binary.__init__(self, **kwd)
+        self._magic_number = b'VELD'
+
+    def sniff(self, filename):
+        # Match the keyword 'VELD' at position 4 or 8 - intsize dependent
+        # Not checking for endianness
+        try:
+            with open(filename, 'rb') as header:
+                intsize = 4
+                header.seek(intsize)
+                if header.read(intsize) == self._magic_number:
+                    return True
+                else:
+                    intsize = 8
+                    header.seek(intsize)
+                    if header.read(intsize) == self._magic_number:
+                        return True
+            return False
+        except Exception:
+            return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = "Binary CHARMM velocity file"
+            dataset.blurb = nice_size(dataset.get_size())
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except Exception:
+            return "Binary CHARMM velocity file (%s)" % (nice_size(dataset.get_size()))
+
+
 class DAA(Binary):
     """
     Class describing an DAA (diamond alignment archive) file