I ran Seurat version 3.1.2 on UseGalaxy, eventhough this toolkit says it can output rds file or R script, but there are no any buttons to save outputs into these datatypes. Is there a way to know how the web interface outputs arguments into the Rscript or rds file?
With version 3.1.2, the new wrapper for seurat outputs in the style of a customizable r markdown instead. You can choose to just have the R code appear in the output via selection at the bottom of the tool. You can have just the graphs, some hybrid of the code and graphs, or all of both on the output file.
@carolyn_nielsen we try to not use rds formats, as they tend to be variant formats with contents we can’t read very well. If you want the datasets in that format, you can use output the datasets alongside the code, then run that in RStudio to retrieve the datasets themselves?
I have just submitted a change in the wrapper to remove that text and avoid confusion. Sorry about that.
@astrov Thanks for the reply- I can try that with my collaborator but I had also wanted to use some of the other Seurat tools within Galaxy that require ‘RDS with a Seurat object’ as the input file.
These look like they are designed for 10X data (mine is plate-based SmartSeq, Nextera Libraries), but may be an option to use the ‘Seurat Read10x’ tool with my tabular counts file to out the RDS object? Should that work without a metadata file?