Adding new generation of table manipulation tools #610
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Do you know this tool? https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute |
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Yes I do ... but the tool is too complex in the form for what it can do and not very flexible. You can't choose specific columns etc. and overall I think it doesn't really cover the use cases. We actually adopted this schema from KNIME which provides very nice tools and operations to perform over tables. |
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I share the concerns of @bgruening and think that (in particular in case of the arithmetics and rename tool) it might be better to extend/improve existing tools.
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| name: tables | |||
| owner: recetox | |||
| remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/analysis" | |||
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The URLs would need fixes
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| <tool id="pandas_arithmetics" name="pandas arithmetics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> | |||
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For this tool I would think that an extension for table compute is more appropriate. The possibility to select specific columns / rows for arithmetic operations would definitely make sense.
| <param argument="--reference_dataset" type="data" format="tabular,csv,tsv,parquet" label="Reference data" help="Reference dataset to use fopr the interpolation" /> | ||
| <param name="x_col" type="data_column" data_ref="reference_dataset" use_header_names="true" label="x (reference)" help="Column from the reference dataset to use as X axis for the interpolator."/> | ||
| <param name="y_col" type="data_column" data_ref="reference_dataset" use_header_names="true" label="y (reference)" help="Column from the reference dataset to use as Y axis for the interpolator."/> | ||
| <param argument="--query_dataset" type="data" format="tabular,csv,tsv,parquet" label="Query dataset" help="Query dataset for which to interpolate the values." /> |
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Are there any constraints regarding the range of the x values of the reference and the query?
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It could be an option to create 1-tool workflows for the tasks where we all the complexity of the the underlying tool gets hidden. |
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@bernt-matthias yes, that is possible - though workflows don't support the column select input type properly, so you can't dynamically select the columns, which massively reduces user friendliness. |
Got it.
This is a point I totally support :) |
This PR introduces a set of new tabular file handling tools which are a bit more modern than what is available in the core galaxy tools.
The tools are based on pandas and/or scipy and all have a python CLI using argparse and should support parquet, csv, tsv and tabular files.
@bgruening and @bernt-matthias and @mvdbeek please give some feedback if you think this design works well or whether it should be done differently. I'm planning to add few more tools to this to cover many use-cases in various -omics disciplines.
Also @KristinaGomoryova please try the tools locally to see if this is roughly what you had in mind.
Also, please let me know whether you would see these tools rather in tools-iuc and if you have a better idea for naming this collection of tools, I'm open to suggestions.