M Bernt

add slash command to trigger IUC CI

4

in conjunction with https://github.com/galaxyproject/tools-iuc/pull/3298

hide injecting several input attributes into behind profile

8

There seem to be better ways to access metadata like dbkey. Also seems error prone since only the first data set is used. As far as I seen these features...

composite data wo primary overwrites other test parameters

15

This loop https://github.com/galaxyproject/galaxy/blob/e1befbd9c570844f1a305d2192c9a8c1a08354f2/lib/galaxy/tool_util/verify/interactor.py#L397 iterates over the inputs of the test and tests if the value is found in the uploads. For composite inputs without primary file this does lead to...

Some problems that I stumbled upon here: https://github.com/galaxyproject/tools-devteam/pull/555 when containerized testing is used: - [ ] `GALAXYROOT/extract_dataset_parts.sh: .venv/bin/activate: line 157: syntax error: bad substitution` - [ ] `/tmp/tmpd3oovgq5/job_working_directory/000/2/task_10/tool_script.sh: line 22:...

Defer evaluation of (dynamic) destinations to allow multiple resubmissions

23

May fix https://github.com/galaxyproject/galaxy/issues/7118 Currently resubmit definitions computed in dynamic destinations get lost because they are not persisted: https://github.com/galaxyproject/galaxy/blob/737775f586c5ab4c4cef4f486dd8826a978ed6b1/lib/galaxy/jobs/handler.py#L215 which (I guess) is a good idea because they are in most...

gff2bed: show that mixed 6/12 col bed is produced

9

seems that the converter produces mixed 6 column / 12 column bed format which makes downstream tools struggle. test data temporarily stored in test-data .. only for demonstration .. I...

Make access to parameters in sections also require full path

39

So far the access to values of parameter in sections did not require to specify the full access path. For ``` ``` in format_source just `par` was used. With the...

With galaxyproject/galaxy#12724 planemo lint may error on input parameters that are not used: - [ ] chemicaltoolbox/openbabel/ob_filter.xml - hbd_min - hbd_max - hba_min - hba_max - psa_min - psa_max -...

split files to collection by delimiter content

1

Just an idea as follow up to https://github.com/bgruening/galaxytools/pull/892 One might extend the generic filter to split by the content of the line matching the record delimiter. Similar to splitting tabular...

openbabel convert

5

I'm wondering why the list of input file types is limited to SDF, MOL, MOL2, CML, InChI and SMILES? I would like to convert pdb to sdf which is possible...