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Add new tool gene.iobio #5365

Merged
merged 12 commits into from
Jun 29, 2023
Merged

Add new tool gene.iobio #5365

merged 12 commits into from
Jun 29, 2023

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JasperO98
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@JasperO98 JasperO98 commented Jun 20, 2023

FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

We added the gene.iobio tool to Galaxy based on creating URLs. Before we wanted to add clin.iobio, but it will not be supported in the long term and gene.iobio was the part of clin.iobio that we actually wanted to have. Related PRs: usegalaxy-eu/temporary-tools#26

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@hexylena hexylena left a comment

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Some linting comments. I'm not sure we can write a sensible version command here without curl which feels wrong.

tools/geneiobio/geneiobio-iframe.xml Outdated Show resolved Hide resolved
<tests>
</tests>
<help><![CDATA[
Gene.iobio provides a report of impactful variants. Gene.iobio also helps prioritize variants based on multiple integrated gene:disease association algorithms and knowledge bases.
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I guess we should be very clear that data is transferred to their servers, since maybe with an iframe it isn't immediately obvious. We could add a warning in the help text

.. class:: Warning mark

This transfers data to a remote server, in US jurisdiction

(with the correct indentation of course)

alternatively maybe that could be a mandatory checkbox that the user has to check to acknowledge? I just worry with such a useful tool for human data someone makes a mistake a bit.

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But in order to use the tool you'd need to make the history public right? I would say that's quite clear, but indeed we'll need to mention it here

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yes, that's true, we don't mention that somewhere, we should mention that as well.

tools/geneiobio/geneiobio-iframe.xml Outdated Show resolved Hide resolved
tools/geneiobio/geneiobio-iframe.xml Show resolved Hide resolved
@bgruening
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@hexylena is this ready to go?

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@hexylena hexylena left a comment

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Yes, looks good, let's ship it.

@hexylena hexylena merged commit b5dd06c into galaxyproject:main Jun 29, 2023
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3 participants