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Merge pull request #16255 from astrovsky01/visium_datatype

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Add Visium datatype for squidpy and spatialomics tools
This commit is contained in:
John Davis
2023-06-20 13:20:39 -04:00
committed by GitHub
parent 6224748f8f 3be998011e
commit d5920c6d78
2 changed files with 24 additions and 0 deletions
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lib/galaxy/config/sample/datatypes_conf.xml.sample
+1
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@@ -185,6 +185,7 @@
<datatype extension="grib" type="galaxy.datatypes.binary:Grib" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="visium.tar.gz" type="galaxy.datatypes.binary:Visium" subclass="true" display_in_upload="true" description="Visium is a tar.gz archive with at least a 'Spatial' subfolder, a filtered h5 file and a raw h5 file." />
<datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
lib/galaxy/datatypes/binary.py
+23
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@@ -318,6 +318,29 @@ class Meryldb(CompressedArchive):
return False
class Visium(CompressedArchive):
"""Visium is a tar.gz archive with at least a 'Spatial' subfolder, a filtered h5 file and a raw h5 file."""
file_ext = "visium.tar.gz"
def sniff(self, filename: str) -> bool:
"""
Check data structure:
Contains h5 files
Contains spatial folder
"""
try:
if filename and tarfile.is_tarfile(filename):
with tarfile.open(filename, "r") as temptar:
_tar_content = temptar.getnames()
if "spatial" in _tar_content:
if len([_ for _ in _tar_content if _.endswith("matrix.h5")]) == 2:
return True
except Exception as e:
log.warning("%s, sniff Exception: %s", self, e)
return False
class Bref3(Binary):
"""Bref3 format is a binary format for storing phased, non-missing genotypes for a list of samples."""