tools-iuc autocycler suit

FOR CONTRIBUTOR:

[x] I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
[x] License permits unrestricted use (educational + commercial)
[x] 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)

This is a collection of tools for Autocycler - https://github.com/rrwick/Autocycler .

Aug 27 '25 08:08 mthang

@bernt-matthias Can you review this autocycler suite and merge it when you can. Many thanks

Sep 23 '25 03:09 mthang

@bernt-matthias Thank you for reviewing the tools . I am working on the improvements at the moment and will resubmit them when I am done.

Sep 26 '25 05:09 mthang

@mthang please ping us when you think a new review is needed :)

Thanks a lot this looks great!

Oct 04 '25 14:10 bgruening

@bgruening @bernt-matthias It took me a while to fix the wrapper and the test-data. Can you please review the wrappers again. Many thanks.

Oct 15 '25 13:10 mthang

The shed.yml was for some reason broken, tests are now running. Lets see what happens :)

Thanks a lot @mthang

Oct 15 '25 14:10 bgruening

Hi @mthang I took some time to rewrite quite a bit to have a more Galaxy look-and-feel, i.e. mainly I removed the nested collectiond and split collections containing fasta and gfa.

What do you think?

Nov 04 '25 15:11 bernt-matthias

Hi @mthang I took some time to rewrite quite a bit to have a more Galaxy look-and-feel, i.e. mainly I removed the nested collectiond and split collections containing fasta and gfa.

What do you think?

Hi @bernt-matthias My apologies for the late reply. This message went under my radar. Please feel free to refactor the wrapper where appropriate. The main reason I made nested collection was due to the fact that Autocycler has a collection of tools. Some tools expect certain output format, so I simpy replicated the logic that Autocycler implemented.

Nov 30 '25 23:11 mthang