Feature/scanpy_mtx_compression #259
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irisdianauy
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Tests using the option have not yet been added |
| </data> | ||
| <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes"> | ||
| <data name="barcodes_10x" label="${tool.name} on ${on_string}: 10x barcodes"> |
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I would have multiple outputs, each attached to a potential value of the format.
| <filter>export_mtx</filter> | ||
| <actions> |
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It might be that these actions require a higher profile than 18.01?
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Thank you, I'll check this.
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Locally passing tests, but still getting the warning below for compression types gz, bz2, and zst. |
irisdianauy
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Great work @irisdianauy . I suspect that Galaxy doesn't support yet the zst compressed format. Do we need it forcefully? |
| <data name="genes_10x_bz2" label="${tool.name} on ${on_string}: 10x genes (bz2)" from_work_dir="genes.tsv.bz2"/> | ||
| <data name="barcodes_10x_bz2" label="${tool.name} on ${on_string}: 10x barcodes (bz2)" from_work_dir="barcodes.tsv.bz2"/> | ||
| </collection> | ||
| <collection name="mtx_zstd" type="list" format="zst"> |
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I cannot find zst support in Galaxy, I would suggest that we comment this part. If we really need it, we could add it as a format to the galaxy codebase (it is called a datatype in Galaxy-speak).
| @@ -1,10 +1,12 @@ | |||
| <macros> | |||
| <token name="@TOOL_VERSION@">1.8.1+3</token> | |||
| <token name="@TOOL_VERSION@">1.8.1+4</token> | |||
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We need to move out of this pattern as it confuses the tools sorting. Please remove the + here and simply bump the Galaxy build number for the tools.
| 1.8.1+4+galaxy0: Upate to scanpy-scripts 1.1.5 (running scanpy ==1.8.1), including an option to compress MTX outputs. | ||
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| 1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper. | ||
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| 1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc. |
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| 1.8.1+4+galaxy0: Upate to scanpy-scripts 1.1.5 (running scanpy ==1.8.1), including an option to compress MTX outputs. | |
| 1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper. | |
| 1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc. | |
| 1.8.5+galaxy0: Update to scanpy-scripts 1.1.5 (running scanpy ==1.8.1), including an option to compress MTX outputs. | |
| 1.8.1+3+galaxy0: Update to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper. | |
| 1.8.1+2+galaxy0: Update to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc. |
or perhaps just change the minor version.
| <option value="zip">zip</option> | ||
| <option value="gzip">gzip</option> | ||
| <option value="bz2">bz2</option> | ||
| <option value="zstd">zstd</option> |
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if zst is not supported in Galaxy then we should remove it for now.
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There are still a number of comments from my last review that haven't been addressed. |
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In particular the versioning pattern is a no go. Also, this should be rebased with Dev please. |
Add compression options to scanpy galaxy tools