Uploaded RDS files are not visible as input in Seurat tools

[a.h.s]

Hello,

I want to use a dataset from GEO for my own analysis. For this, I downloaded the file “GSE135893_ILD_annotated_fullsize.rds.gz” to galaxy. The file is described as “Annotated Seurat Object” and in galaxy the format is detected as rds after download.

Now, when I want to use it as the input for another Seurat tool that expects an .rds file as input (like Seurat Plot dimension reduction), the downloaded file is not available as an input.

What could be the reason for this?

Thank you a lot!

[jennaj]

Welcome, @a.h.s

@a.h.s

Now, when I want to use it as the input for another Seurat tool that expects an .rds file as input (like Seurat Plot dimension reduction), the downloaded file is not available as an input.

Where are you using Galaxy? At a public server (URL please) or a private server?

I just see one Seurat tool at public servers, so I’m guessing that the tool wrapper was written independently? It might have a problem with the datatype filter. That would need to be reported to whoever wrote the tool.

Try this to see what assigned datatype(s) the tool is expecting to process, then compare that with the datatype assigned to your input datasets.

@jennaj

There are some tools that expect just fastq or fastq.gz (scaling unspecified). But if you are ever not sure what datatype(s) a tool accepts as input, any tool not just those that accept reads, try this:

1. Create a new empty history
2. Load up the tool form
3. Review the input datatypes listed in the tool form’s input area
4. Note: A tool could have more than one input area and this works for all user-supplied inputs from the history.

Example

[pavanvidem]

Please gunzip it and then try setting the format to rdata.