add: metaMDBG wrapper

[Kulik7]

Adding tool wrapper based on request #6578

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)

[bernt-matthias]

Great Start. I added a few comments. The use of $__tool_directory__ needs to be fixed.

[bernt-matthias]

I think the conditional is not really needed. Just a data and select parameter should be sufficient.

[bernt-matthias]

Do you have a test for the other type?

[Kulik7]

Not really, should I make one?

[bernt-matthias]

Instead of name="contigpath" use argument="--contigpath". This will also create the variuable $contigpath for the command block and additionally add (--contigpath) to the parameter help (then the user knows whioch Galaxy parameter controls which CLI ragument).

[martenson]

started in 5628499

[Kulik7]

Thank you for the comments, I tried to work on the suggestions.
I was also trying to come up with test-files that would fit the size requirments, but I'm not sure it's possible to have a working example for MetaMDBG under 1 MB.

[martenson]

the tests for metamdbg pass for me locally in biocontainer, however metamdbg gfa ends with the same segfault as in github ci (visible at https://github.com/galaxyproject/tools-iuc/actions/runs/15249225749)

Job in error state.. tool_id: metamdbg_gfa, exit_code: 139, stderr: 
	Assembly dir: .
	Used k: 21
	Homopolymer compression: 0
	Data type: 1

Generating unitig sequences
Loading unitig sequences
Creating assembly graph file
/tmp/tmpxsakc5w0/job_working_directory/000/4/tool_script.sh: line 23:     9 Segmentation fault      (core dumped) metaMDBG gfa --assembly-dir . --k 21 --threads "${GALAXY_SLOTS:-1}"
.

[martenson]

manually running the metamdbg gfa test on the outputs of metamdbg runs fine locally

[bgruening]

@martenson anythig I can help here? Is conda working and containers are crashing? Or what is the problem?

[martenson]

@bgruening container works fine, I just need to have a closer look at the test, should have time next week