Bug with trimal 1.5.0+galaxy1

[jennaj]

https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal

The first tool test is reporting this error at UseGalaxy.eu -- seems to have trouble reading in the mfa input file. Works fine version 1.5.0+galaxy0.

ERROR: Alignment not loaded: "/data/dnb11/galaxy_db/files/1/2/3/dataset_123ba341-a873-42d0-a545-1903205f02b0.dat" Check the file's content.

Reported at https://help.galaxyproject.org/t/trimal-use-inputfiel/15967

Test history https://usegalaxy.eu/u/jenj/h/test-trimal

[wm75]

@jennaj I don't quite understand what you did in that test history. You seem to have selected a dataset 2 from a different history as input, which is in .yaml format and according to the server has the following content:

assembly:
  accession: GCA_018777385.1
  alias: Candidatus Symbiopectobacterium
  bioproject: PRJEB12068
  biosample: SAMN17910462
  record_type: assembly
taxon:
  name: SAMN17910462
  id: 801

So unsurprisingly this will fail to get parsed as an AA alignment input. The tool seems to be working fine when run on the correct input.
Please let me know if you wanted to demonstrate something else with that history.

[bernt-matthias]

which is in .yaml format

Maybe we should remove txt from the list of accepted formats?

[jennaj]

I don't quite understand what you did in that test history.

Me either! I loaded up the tool test from generate tour. Probably working too fast, was in the user history, then used "switch to history". Switching histories maybe should "forget" about potential input datasets (I notice this but am possibly switching way more than regular users)? But I'm really sorry for wasting time here!

[bernt-matthias]

No worries. Thanks for the feedback.

Then we only need to decide if txt should remain a valid input format .. or close this.