M Bernt

The current code causes a stack trace for some calls, eg. ` enasearch retrieve_taxons --ids 'Elusimicrobia:phylum' --result 'coding_release' --display 'fasta' --download 'fasta' ` (probably the call is missing something anyway...

Unused tool parameters

1

Tools that define input parameters that are not used in the command or anywhere else: - [ ] tools/hisat/hisat.xml - ignore_quals - min_intron - max_intron In this case the tool...

gi2taxonomy seems outdated

3

The tool depends on package_taxonomy_1_0_0 which seems to be replaced by data_manager_fetch_ncbi_taxonomy. Furthermore the data for the tool data is hard coded in the python file: see GI2TAX, NAME_FILE, NODE_FILE....

https://help.galaxyproject.org/t/crex-missing-header-error/12481/2

Kaiju

2

https://github.com/bioinformatics-centre/kaiju

Latest suite_xcms in the TS 28:cb165d5e69b5 includes msnbase_readmsdata 86a20118e743. But the latest msnbase_readmsdata is 12:f6b2750ea32e.

xcmsSet problem

3

When using xcmsSet with ``` Scan range option | hide |   Extraction method for peaks detection | centWave |   Max tolerated ppm m/z deviation in consecutive scans in ppm |...

**Describe the bug** For integer parameters with - only `max` (positive value) defined: - one gets a slider allowing to select values between 0 and max (when lowered with the...

Export citations exports citations also for deleted datasets

3

**Describe the bug** If I export citations from a history I also get citations from deleted datasets. I noticed this for the tool `Split file to dataset collection`. See this...

As suggested here https://github.com/galaxyproject/galaxy/pull/16495 but not used here https://github.com/galaxyproject/galaxy/pull/16542 .. even if it does not run (unfortunately) https://github.com/galaxyproject/galaxy/pull/16495#issuecomment-1658631173 ## How to test the changes? (Select all options that apply) -...