Add CountESS tool#7967
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waiting for bioconda recipe for CountESS |
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Bioconda available, tests started. |
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@bgruening we also need bioconda for
These packages are not available from |
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Can we patch those dependencies out? If not I think we would need to get them into conda-forge. If this is too complicated fallback to a container. |
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@bgruening I patched them out, when you have time, could you review bioconda/bioconda-recipes#65263 |
wm75
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wm75
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Puh, not easy to review without knowing countess very well. Couple of questions:
- Is there ever a case where one countess workflow input node has more than one input file? From the examples it seems as if workflows always start with Load nodes that load individual files?
- Are those input nodes input files always called
files.0.filename, etc.? - All modules seem to be plugin based. Are all those plugins provided by the bioconda recipe, or could a countess workflow depend on custom plugins that are then not available to the bioconda package/Galaxy?
| <repeat name="output_mappings" title="Output file mapping" min="1" default="1" help="Map CountESS save-node filename parameters into a Galaxy output collection."> | ||
| <param name="node_name" type="text" label="CountESS save node name" help="For example: CSV Save 5. This must match the node name in the CountESS INI file."> | ||
| <validator type="empty_field"/> | ||
| </param> | ||
| <param name="parameter_name" type="text" value="filename" label="CountESS output filename parameter" help="E.g., filename."> | ||
| <validator type="empty_field"/> | ||
| </param> | ||
| <param name="output_filename" type="text" value="output.csv" label="Output filename" help="Relative filename to write into the Galaxy output collection. Use extensions like .csv, .tsv, or .txt for datatype detection."> | ||
| <validator type="empty_field"/> | ||
| </param> | ||
| </repeat> |
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why are output_mappings needed? What's wrong with just processing/sanitizing the names in the original .ini file?
1-2. Yes, a CountESS load node can contain multiple input files. CountESS represents load-node files as an array in the .ini file, e.g. files.0.filename, files.1.filename, files.2.filename (https://github.com/CountESS-Project/CountESS/blob/main/docs/config-file-format/index.md#plugin-configuration). This is implemented by the CountESS DuckdbLoadFilePlugin base class using FileArrayParam("Files", LoadFileMultiParam("File")). The Galaxy wrapper supports this by allowing multiple input mapping repeats. Users can map several Galaxy datasets to the same CountESS input node by setting parameter names such as files.0.filename, files.1.filename, etc.
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FOR CONTRIBUTOR:
There are two labels that allow to ignore specific (false positive) tool linter errors:
skip-version-check: Use it if only a subset of the tools has been updated in a suite.skip-url-check: Use it if github CI sees 403 errors, but the URLs work.