Groot update DM path

[hugolefeuvre]

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)
  DM path was not the same in command wrapper and json file

[bernt-matthias]

What's wrong with the old path?

[hugolefeuvre]

What's wrong with the old path?

In the command part of the DM xml, data are downloaded into a repository called arg-annot.90 (in the case of arg-annot database), but in the json, at the end the path was in a repository called groot_database/data/arg-annot.90-1.1.2-13112024.
I'm not sure if the error stems from that, but it's the only difference with the tests I run in the tools section. The tool was integrated into Galaxy because the tests passed but once on the platform I encounter an error, you can find them here : https://usegalaxy.fr/u/hugo-lefeuvre/h/test-groot

[bernt-matthias]

From your failing job it seems that the tool using the data tries to access tool-data/groot_database/data/arg-annot.90-1.1.2-13112024 which is not what the new version creates.

I definitely miss the groot_database/ part of the tool.

[bernt-matthias]

Likely the problem is that the data manager tool needs to place the files in a directory $out_file.extra_file_path instead of the job working directories.

I made the same error in a few data managers. See the fix here Helmholtz-UFZ/galaxy-tools#71

[bernt-matthias]

I guess in the config file you need to replace

- "path": "/$database.$identity",
+ "path": "$database.$identity",

[hugolefeuvre]

Likely the problem is that the data manager tool needs to place the files in a directory $out_file.extra_file_path instead of the job working directories.

I made the same error in a few data managers. See the fix here Helmholtz-UFZ/galaxy-tools#71

I made the change in the last commit, hope I've done it right

[bernt-matthias]

Looks good to me. Last thing to do is to increase VERSION_SUFFIX

[bernt-matthias]

Sorry. Must have overlooked this :)

[hugolefeuvre]

Sorry. Must have overlooked this :)

No problem, thanks for the review !