hide ebi scanpy tools #1662
hide ebi scanpy tools #1662
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| <section id="single-cell" name="Single-cell"> | ||
| <tool file="/opt/galaxy/custom-tools/ebi-gxa/scanpy-parameter-iterator.xml" hidden="True" /> | ||
| <tool file="/opt/galaxy/custom-tools/ebi-gxa/scanpy-plot-trajectory.xml" hidden="True" /> | ||
| <tool file="/opt/galaxy/custom-tools/ebi-gxa/scanpy-compute-graph.xml" hidden="True" /> |
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Thanks @nilchia
I don't think we have all the scanpy functions on IUC. We should keep at least the 3 EBI tools that @bgruening pointed.
Also for now, let's keep the episcanpy because the preprocessing tutorial seems to be still in use.
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The compute-graph can be done by Scanpy Inspect and manipulate pp.neighbors
The plot-trajectory can be done by scanpy plot selecting pl.paga
The parameter-iterator can be skipped but it should be easy to implement it to IUC
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Ok. There is a tutorial on parameter iterator. We should keep it.
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In that training all the EBI tools are used :/
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Btw. I have hidden now all tools.
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Ok, that took some time ... please check in 5min if everything is hidden. There were hundreds of tools (many versions) |
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As discussed at the SPOC meeting with @pavanvidem and @MarisaJL and previously with @nomadscientist 🖖 , we decided to continue with the scanpy IUC tool suite and hide the EBI version.
Currently, it is confusing for the user when they try to search "scanpy" in the tool panel, as many tools will pop up.
@nomadscientist did great work and migrated all the EBI tools of the single cell trainings to the IUC ones.
So it is time to hide EBI scanpy :)
Also the EpiScanpy tool is not maintained anymore, and snapatac2 is the replacement. We also decided to hide this as well.