add bioformats2raw

[bugraoezdemir]

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)

[kostrykin]

Thanks @bugraoezdemir

The linter fails due to an issue with the owner field in the .shed.yml, see my comments for that.

Also, the first test fails when I run planemo test --docker . locally:

bf2raw (Test #1): failed
bf2raw (Test #2): passed
bf2raw (Test #3): passed

The reported problem is:

Expecting value: line 1 column 1 (char 0)

Sorry for the confusion, I didn't want to approve the PR yet, only the changes made recently… misleading UI

[kostrykin]

https://github.com/BMCV/galaxy-image-analysis/actions/runs/6876332188/job/18701807360?pr=72#step:3:22

Files larger than 1M found
tools/bioformats2raw/test-data/filament.tif
tools/bioformats2raw/test-data/xy_12bit__plant.oir
Error: Process completed with exit code 1.

[bugraoezdemir]

https://github.com/BMCV/galaxy-image-analysis/actions/runs/6876332188/job/18701807360?pr=72#step:3:22

Files larger than 1M found
tools/bioformats2raw/test-data/filament.tif
tools/bioformats2raw/test-data/xy_12bit__plant.oir
Error: Process completed with exit code 1.

OK, I will replace them with smaller files.

[bugraoezdemir]

https://github.com/BMCV/galaxy-image-analysis/actions/runs/6876332188/job/18701807360?pr=72#step:3:22

Files larger than 1M found
tools/bioformats2raw/test-data/filament.tif
tools/bioformats2raw/test-data/xy_12bit__plant.oir
Error: Process completed with exit code 1.

OK, I will replace them with smaller files.

@kostrykin I have changed the test data.

[kostrykin]

Thanks, @bugraoezdemir!

Regarding this, I tried changing the output format to ome.zarr, which works (the tests pass), but there is a warning:

WARNING:galaxy.model:Datatype class not found for extension 'ome.zarr'

I'm not sure what the state of this is in Galaxy. Shall we keep it on html or change to ome.zarr?

[bugraoezdemir]

Thanks, @bugraoezdemir!

Regarding this, I tried changing the output format to ome.zarr, which works (the tests pass), but there is a warning:

WARNING:galaxy.model:Datatype class not found for extension 'ome.zarr'

I'm not sure what the state of this is in Galaxy. Shall we keep it on html or change to ome.zarr?

@kostrykin The fact that it passes the tests is a bit deceptive. I have locally tested it with planemo serve and the output was an empty file. So I would suggest that we keep this version with html and when ome.zarr is fully established as a Galaxy data type, we can update the tool accordingly.

[bgruening]

ome.zarr is unfortunately not ready yet as a datatype :(

[kostrykin]

Alright, thank you all!

[kostrykin]

Deployment to toolshed failed due to the following error:

Could not update bioformats2raw
Failed to find repository for owner/name euro-bioimaging/bioformats2raw
Repository bioformats2raw updated successfully.
Could not update bioformats2raw
Failed to find repository for owner/name euro-bioimaging/bioformats2raw
Unexpected HTTP status code: 400: {"err_msg": "You already own a repository named bioformats2raw, please choose a different name.", "err_code": 400008}
Repository [bioformats2raw] does not exist in the targeted Tool Shed.
Failed to update metadata for repository 'bioformats2raw' on the main Tool Shed.
Repository contents updated but failed to update metadata for repository 'bioformats2raw' on the main Tool Shed.

https://github.com/BMCV/galaxy-image-analysis/actions/runs/6879105347/job/18710524827#step:6:224

I find the error message somewhat confusing. @bgruening You maybe know what this means?

My interpretation is that "Failed to find repository for owner/name euro-bioimaging/bioformats2raw" is the root cause? Does such a repository exist in the ToolShed?