I am a bit new in galaxy and I am currently trying to adapt a stand alone program (written in R) into galaxy tools.
To communicate beatween the tools, I am using RDS files but I struggle a bit to read them once they are loaded in galaxy.
following this post using R data structure files (rds) as input/output in galaxy tools and some github code from Stef van Lieshout, I was able to create a rds type that is correctly uploaded in galaxy but when I try a readRDS() in R script, it fails to load them into the script.
I tried to read the data file as galaxy display it (in galaxy/database/files/000/dataset_anID.dat) and it is obviously something R won't read with readRDS (it is not a binary)
so I am a little bit lost on how I should handle this. Is the following pipeline correct or did I miss something ?
- declaring a new datatype as explained in the link above
- uploading a rds file in galaxy
- using this data as input of my R-based tool
- using readRDS() in the R code to load the file