galaxyproject
New SCEasy Converter tool doesn't recognise datasets in the history
I do realise that SCEasy Converter is now new so maybe that's still something in the development stage, but currently it is not possible to select any datasets from the history as the input - shown below.
@mtekman @pavanvidem
Oh whoops. I thought I tested the UI, but I think that was before the container melodrama I was experiencing at the time.
@wee-snufkin Does it do anything if you forcibly drag and drop a dataset in there?
Then it says (unavailable) but the tool runs successfully, and the output dataset looks correct.
I've checked the 'forced' conversion AnnData <-> Seurat and the Seurat output is recognisable by the respective tools however AnnData output is in .h5 format that the Inspect AnnData tool doesn't recognise. I tried to change the datatype to .h5ad but metadata generation failed with the following error message:
Loading required package: reticulate Loading required namespace: Seurat Warning message: In .regularise_df([email protected], drop_single_values = drop_single_values) : Dropping single category variables:orig.ident, Sample.Characteristic.organism., Sample.Characteristic.Ontology.Term.organism., Sample.Characteristic.strain., Sample.Characteristic.Ontology.Term.strain., Sample.Characteristic.developmental.stage., Sample.Characteristic.Ontology.Term.developmental.stage., Sample.Characteristic.age., Sample.Characteristic.Ontology.Term.age., Sample.Characteristic.Ontology.Term.individual., Sample.Characteristic.Ontology.Term.genotype., Sample.Characteristic.organism.part., Sample.Characteristic.Ontology.Term.organism.part., Sample.Characteristic.cell.type., Sample.Characteristic.Ontology.Term.cell.type., Factor.Value.Ontology.Term.genotype.
Thanks for testing this! If you force the h5 input into the "Inspect Anndata" tool, without converting it to h5ad, does the "Inspect Anndata" tool produce anything?
Ha, yes - it works then! Produces an output dataset without any problems.
Phew! Okay, then it's just a naming issue with the file formats. I will try to make a quick edit.
Could you give me a dataset or share a history for me to test with?
Sure, here it is: https://usegalaxy.eu/u/j.jakiela/h/copy-of-anndata---seurat