I uploaded some data and organised it into a collection but I noticed that I selected the wrong datatype. Is there a way to change the datatypes of all elements of a collection (and thus have the dataset collection’s type change)?
There was a new feature introduced into release
21.09 to do this. You’ll need to switch over to the “Beta” history view to use it.
Details are here: September 2021 Galaxy Release (v 21.09) — Galaxy Project 21.09.1.dev0 documentation
Note that this will only work for changing the datatype if there is an existing “convert” tool to do the transformation. Here is an example where I had to convert to from
bed > csv > tabular – as a direct
bed > tabular wasn’t available (Why?
bed format is already within the scope of
tabular format so there isn’t a specific convert operation for it). Galaxy | Accessible History | test collection datatype change
Hope that helps
Thanks for the tip, but unfortunately that converts data between datatypes, as you said, using a converter tool. In the single-item dataset editor one can change the datatype without running a converter - so e.g. fastq.gz to fastqsanger.gz. So it seems that there still isn’t an option to do what I’m looking for (I uploaded some FASTQ data and it was auto-assigned to fastq.gz when the workflow I wanted to use required fastqsanger.gz). Seems that I’ll have to make a feature request…
Bulk operations are on the to do list for the beta history, and I’d think that would include format changes, @dannon ?
@pvanheus - I had this same problem recently too. My solution involved creating a workflow that then set the output type on the collection.
(Edit: though I’m not sure if this invokes the converter or sets the datatype…)
Very clever!! That is directly assigning the datatype, which is what Peter wants to do as well.
I expect that the collection metadata editing functions will have the “Datatype” tab added. It is a popular enhancement request. Related tickets: 12725 && 8013