Marius van den Beek comments

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                                            Marius van den Beek

Tool test runs despite not giving input datasets to mandatory data parameter

We should explore sending an explicit null here. This test would likely be invalid with a newer galaxy profile version.

Publication of Galaxy Release v 25.0

https://github.com/galaxyproject/galaxy/pull/19892 needs a deprecation notice. We also wanted to add tests against iuc and iwc before the usegalaxy.org update.

AttributeError: 'str' object has no attribute 'file'

The tool in question is toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6

AttributeError: 'str' object has no attribute 'file'

Thanks for looking at this, but no matter if it is a tool bug or not, there is a Galaxy and/or Pulsar bug here. We can't fail like this.

AttributeError: 'str' object has no attribute 'file'

I saw that, and that is in fact why I reopened this. Can you confirm that you agree that we can't post strings where we expect files, independently of invalid...

Add Metaproteomics GTN workflow

``` Tue Dec 10 10:57:25 GMT 2024 Reading identification files. Tue Dec 10 10:57:25 GMT 2024 No identifications retained. Tue Dec 10 10:57:25 GMT 2024 PeptideShaker Processing Canceled. PeptideShaker processing...

dada2 use default_identifier_source

yes

dada2 use default_identifier_source

Thank you @bernt-matthias!

integrate actc

If the tool produced unsorted bam and that's what consumed in a following step you can also set the format to `unsorted.bam`

h5web visualisation doesn't work

That should have been fixed in #18552