M Bernt
Might it be that you should ```diff - if args.danglingSequence: + if args.restrictionCutFile ``` over here: https://github.com/deeptools/HiCExplorer/blob/c1e9e92773770dad6ddb002ed7f8522b1dfa56ca/hicexplorer/hicQuickQC.py#L120 But all theses if statements might be dropped anyway since the arguments of...
I would need to get a container for this tool. We could add the ASaiM repo to planmeo-monitor, but the repo seem dead. Also this seems in line with: https://github.com/bgruening/galaxytools/pull/1248...
``` 1 ConditionalOptionMissing 1 HelpEmpty 1 InputsBoolDistinctValues 1 InputsSelectOptionalRadio 1 OutputsNameDuplicated 1 RequirementVersionMissing 1 TestsOutputCheckDiscovered 1 TestsOutputName 1 ToolNameWhitespace 1 ToolVersionPEP404 2 InputsMissing 2 InputsSelectOptionDuplicateText 2 OutputsNameInvalidCheetah 3 CommandInterpreterDeprecated 3...
Here I started a tutorial o how Galaxy processes dataset(s). I think it's important that users understand. It also should describe how to map over for tools that process multiple...
Due to the change in Anaconda Inc's TOS many institutions do not allow to use conda's `default` channel. Since miniconda uses `default` (e.g. for setting up the base environment and...
The [QC step](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html#comment-4) of the tutorial suggests to upload the html results of QUAST. This does not work: https://github.com/galaxyproject/galaxy/issues/19220 also the results are not available as data library (or I...
When creating the Galaxy wrappers for kaiju I noticed that the parameter -u seems to be inconsistent between kaiju2table and kaiju2krona: - `-u Unclassified reads are not counted for the...
TODO: - [ ] check if `fasta.bz2` really works and if so add auto compressed datatype to Galaxy - [ ] yes: https://github.com/galaxyproject/galaxy/pull/20496 FOR CONTRIBUTOR: * [x] I have read...
and also allow to use legacy data. We have to do this because the old datatable may contain entries that are not usable without the `--mpa3` flag. Alternatively we could...