Merge pull request #8964 from simonbray/gmx

Add new GROMACS datatypes: ndx, xvg, edr

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -641,8 +641,11 @@
     <datatype extension="top" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="itp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="mdp" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
+    <datatype extension="ndx" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
+    <datatype extension="xvg" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
     <datatype extension="xtc" type="galaxy.datatypes.binary:Xtc" display_in_upload="true"/>
     <datatype extension="cpt" type="galaxy.datatypes.binary:Cpt" display_in_upload="true"/>
+    <datatype extension="edr" type="galaxy.datatypes.binary:Edr" display_in_upload="true"/>
     <datatype extension="gro" type="galaxy.datatypes.tabular:Tabular" subclass="true" 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"/>
@@ -821,6 +824,7 @@
     <sniffer type="galaxy.datatypes.binary:Dcd"/>
     <sniffer type="galaxy.datatypes.binary:Xtc"/>
     <sniffer type="galaxy.datatypes.binary:Cpt"/>
+    <sniffer type="galaxy.datatypes.binary:Edr"/>
     <sniffer type="galaxy.datatypes.binary:Vel"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>

lib/galaxy/datatypes/binary.py

@@ -957,7 +957,7 @@ class Trr(GmxBinary):
     """
 
     file_ext = "trr"
-    magic_number = 1993  # magic number reference: https://github.com/gromacs/gromacs/blob/1c6639f0636d2ffc3d665686756d77227c8ae6d1/src/gromacs/fileio/trrio.cpp
+    magic_number = 1993  # magic number reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/trrio.cpp
 
 
 class Cpt(GmxBinary):
@@ -994,6 +994,23 @@ class Xtc(GmxBinary):
     magic_number = 1995  # reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/xtcio.cpp
 
 
+class Edr(GmxBinary):
+    """
+    Class describing an edr file from the GROMACS suite
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('md.edr')
+    >>> Edr().sniff(fname)
+    True
+    >>> fname = get_test_fname('md.trr')
+    >>> Edr().sniff(fname)
+    False
+    """
+
+    file_ext = "edr"
+    magic_number = -55555  # reference: https://github.com/gromacs/gromacs/blob/cec211b2c835ba6e8ea849fb1bf67d7fc19693a4/src/gromacs/fileio/enxio.cpp
+
+
 class Biom2(H5):
     """
     Class describing a biom2 file (http://biom-format.org/documentation/biom_format.html)