Decoupler pathways inference from differential expression files #339
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anilthanki
reviewed
Nov 29, 2024
| # read in the AnnData input file | ||
| adata = ad.read_h5ad(args.input_anndata) | ||
| # detect based on input file extension if the input file is AnnData or matrix | ||
| if args.input.endswith(".h5ad"): |
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how about input file with .h5 extension
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It is not needed, since this is internally controlled with the galaxy wrapper, which will transform the filename forcefully into input.h5ad . Also the extension .h5 is generally used for any HDF5 file, not just AnnData, the community tends to favour .h5ad for anndata (although it is just a convention).
anilthanki
reviewed
Nov 29, 2024
|
Last commit broke the python linting, I don't think is really worth it, so I will reverse it. |
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Description
This enables the decoupler pathways inference tool to run from differential expression tsv files.
Type of change
Checklist
@TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g.@TOOL_VERSION@+galaxy0)@TOOL_VERSION@+galaxy0@TOOL_VERSION@+galaxy1). It is acceptable to do this as well when the cli version changed but not the underlying tool (to avoid issues in the coming point).@TOOL_VERSION@part of the version does not contain any+symbols within, otherwise this will break tool ordering on the interface and the default tool being picked. Tool version should always conform to PEP440 to avoid this issue. The only+should be the one precedinggalaxy<build>(unless that all the versions from that tool previously followed a different pattern).