Merge pull request #17499 from martenson/clean-magres

[23.2] Add magres datatype

CONTRIBUTORS.md

@@ -74,6 +74,7 @@ The following individuals have contributed code to Galaxy:
 * Björn Grüning <[email protected]> <[email protected]>
 * Aysam Guerler <[email protected]>
 * Simon Guest <[email protected]>
+* Nalin Gupta <[email protected]>
 * Jianbin He <[email protected]>
 * Peter van Heusden <[email protected]>
 * Morita Hideyuki <[email protected]>

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

@@ -778,10 +778,11 @@
     </datatype>
     <datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
     <datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
-    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true"/>
-    <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true"/>
-    <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true"/>
-    <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true"/>
+    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true" description="The .cell file contains geometry information, including cell parameters, atomic coordinates, and k-point coordinates and weights. The file consists of lines containing keywords and data blocks, and associated values" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfilecell.htm"/>
+    <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true" description="CIF or Crystallographic Information File is the standard format for storing crystallographic structural data" description_url="https://www.iucr.org/resources/cif"/>
+    <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true" description="Basic format for atomic positions in a structure" description_url="https://open-babel.readthedocs.io/en/latest/FileFormats/XYZ_cartesian_coordinates_format.html"/>
+    <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true" description="Extended XYZ format is an enhanced version of the basic XYZ format that allows extra columns to be present in the file for additonal per-atom properties as well as standardising the format of the comment line to include the cell lattice and other per-frame parameters" description_url="https://wiki.fysik.dtu.dk/ase/ase/io/formatoptions.html#extxyz"/>
+    <datatype extension="magres" type="galaxy.datatypes.molecules:Magres" display_in_upload="true" description="Ab initio Nuclear Magnetic Resonance file format providing a complete archival and data processing format for the results of first principles calculation of NMR parameters" description_url="https://www.ccpnc.ac.uk/docs/magres"/>
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true">
       <converter file="mdconvert.xml" target_datatype="xtc"/>
       <converter file="mdconvert.xml" target_datatype="dcd"/>
@@ -962,9 +963,9 @@
     <datatype extension="storm.check" type="galaxy.datatypes.text:StormCheck" display_in_upload="true"/>
     <datatype extension="ctl.result" type="galaxy.datatypes.text:CTLresult" display_in_upload="true"/>
     <!-- CASTEP types -->
-    <datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true"/>
-    <datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true"/>
-    <datatype extension="den_fmt" type="galaxy.datatypes.text:FormattedDensity" display_in_upload="true"/>
+    <datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true" description="numerical output of a CASTEP job in ASCII format" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfilecastep.htm"/>
+    <datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true" description="the param file contains all the input control parameters required to run a CASTEP job. Consists of lines containing keywords and associated values" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfileparam.htm"/>
+    <datatype extension="den_fmt" type="galaxy.datatypes.text:FormattedDensity" display_in_upload="true" description="formatted electronic density file output by CASTEP containing value of electron density for a grid of points"/>
     <!-- Larch types -->
     <datatype extension="prj" type="galaxy.datatypes.larch:AthenaProject" display_in_upload="true" description="Athena project file."/>
     <datatype extension="inp" type="galaxy.datatypes.larch:FEFFInput" display_in_upload="true" description="FEFF input file."/>
@@ -1140,6 +1141,7 @@
     <sniffer type="galaxy.datatypes.molecules:CIF"/>
     <sniffer type="galaxy.datatypes.molecules:ExtendedXYZ"/>
     <sniffer type="galaxy.datatypes.molecules:XYZ"/>
+    <sniffer type="galaxy.datatypes.molecules:Magres" />
     <sniffer type="galaxy.datatypes.molecules:MOL2"/>
     <sniffer type="galaxy.datatypes.molecules:InChI"/>
     <sniffer type="galaxy.datatypes.molecules:FPS"/>