new tool: galaxy wrappers for the pcdl physicell data lader command line commands

[elmbeech]

FOR CONTRIBUTOR:

• [ yes] I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• [ yes] License permits unrestricted use (educational + commercial)
• [ yes] This PR adds a new tool or tool collection
• [ no] This PR updates an existing tool or tool collection
• [ no] This PR does something else (explain below)

[bgruening]

@elmbeech thanks! I added a few comments that apply for all tools. I think a macro file and a proper formatting will help a lot for further reivew.

Please have a look at the Galaxy Language Server, it has some build-in tools for auto-formatting.

[bgruening]

I think this is what you mean with "langauage server". Looks like i have to check my implementation with vscode . ok, i can do that.

* https://github.com/galaxyproject/galaxy-language-server

Could you please point me to what you mean with "macro"? Thank you!

Sure. https://planemo.readthedocs.io/en/latest/writing_advanced.html#macros-reusable-elements
e.g. here: https://github.com/galaxyproject/tools-iuc/blob/main/tools/bedtools/macros.xml

[bgruening]

You can find the xunit/error reports here: https://github.com/galaxyproject/tools-iuc/actions/runs/16511690042?pr=7034

When one test files with error code 1, planemo should not fail, you probably want to know what the others tests do, if they also fail or if only test 1 fails.

[bgruening]

Looking at your error report it seems some test files are missing:

• output00000000_oxygen.jpeg
• timeseries_cell_maxabs.h5ad
• output00000000_cell.csv

etc

[bgruening]

This looks really nice @elmbeech!

I added a bunch of comments that should improve future updates but also UX for the user. Please let me know if you have any questions.

[bgruening]

You need to go to the CI summary page, this one: https://github.com/galaxyproject/tools-iuc/actions/runs/16556891445?pr=7034

Than you see:

you still have a lot of files missing:

Collection element output00000000_cell_maxabs of collection anndata_h5ad: Test output file (output00000000_cell_maxabs.h5ad) is missing. If you are using planemo, try adding --update_test_data to generate it.

[bgruening]

Please see my last comment, I think this explains your failing tests.

[elmbeech]

ogge! now the test are passing :").
the rest is cosmetic. i will do it later this week or over the weekend or so.

[bgruening]

Please let me know when you think you are ready.

[elmbeech]

@bgruening i think it is ready.

[bgruening]

Great, I will try to have a look asap again. This is a really nice set of tools, thanks a lot!

[elmbeech]

thank you for the appreciation!
honestly, i did not expect that it would be that much work and take that much time to write a wrapper for a command line script.
to be fair, i have to say i am not too familiar with all this web framework stuff and had only little knowledge about galaxy dateing some years back.
in any case, happy when all this work ends up in a final and hopefully useful product.
that Randy got the pcstudio in galaxy running (as i understood with help from you too) was very impressive!

[elmbeech]

thank you for all your help with the PR!

[bgruening]

honestly, i did not expect that it would be that much work and take that much time to write a wrapper for a command line script.

You picked the IUC battle, rigorous reviews and annoying dudes that care about UX :)
Your integration was working in the first days, you could deploy that. On IUC we would like to go a few steps ahead and make those integrations readable, usable and maintainable.
I hope it was worth your time.

If you like use select for the colormap and then we are ready to go I think.

[elmbeech]

Thank you, Bjoern!
As I undertook this task, I wanted to do something proper so it was worth the time. And I got help and advice.
I changed to select and re-formated with vscode for a last time.
Now all should be ready.

[bgruening]

Step 3 of https://usegalaxy-eu.github.io/posts/2020/08/22/three-steps-to-galaxify-your-tool/ if you like :)

[bgruening]

Merci!!!

[elmbeech]

hi @bgruening ,

I hope you still see this message.

Somehow, naively, I thought when I merge my tools into the tools-iuc repo, they will become avaliable in at https://galaxy.eu and https://usegalaxy.org/ . But when I am searching for them in the "search tools" bar or in the panel below, I cannot find them.
I definitely can find them in the main toolshed (https://toolshed.g2.bx.psu.edu/), but that's it.

Could you please point me to the documentation where I can learn how to use the pcdl tools online at galaxy eu or usa? Or are these tools only for use on a local installation?

thank you, Elmar

[bgruening]

See my last message, step 3 ;-)

Your tool is now in our App store and can be installed by all admins. However, admins are able to decide what goes in.

[elmbeech]

Thank you Bjoern, for that swift reply!
Totally missed this. I will give it a try in Europe and the US.
Have a good rest of the weekend. Best, Elmar

[elmbeech]

i think first just Europe.
let's see what happens.