add spacexr #6212
add spacexr #6212
Conversation
Co-authored-by: Björn Grüning <[email protected]>
|
Is there another way other than "compare=sim_size" to check ".pdf" and ".rds" outputs? |
tools/spacexr/spacexr_cside.xml
Outdated
| #end for | ||
| #set $final_region = ', '.join($regions) | ||
| #set $final_region = "list(" + ", ".join(f"c({', '.join(map(repr, sublist))})" for sublist in $regions) + ")" |
There was a problem hiding this comment.
this looks wrong ... should final_region be a list() or a sting?
#set is executing a python expression and final_region is a python variable at this point.
There was a problem hiding this comment.
yes, it should be a list.
I tried to do a trick and make an R list within a Python variable so I could use it in the script.
it should be a minimum:
final_region <- list(c("A","B",...),c("C","D",...),c("E","F",...),...)
There was a problem hiding this comment.
Oh ... that is ... interesting :)
There was a problem hiding this comment.
Yes, but now I changed the input as a tabular file.
This makes more sense I guess :)
|
Thanks @nilchia! Please consider writing a news item for this. |
|
Attention: deployment failure! https://github.com/galaxyproject/tools-iuc/actions/runs/12797958414 |
FOR CONTRIBUTOR:
This PR adds spacexr to Galaxy. This tool is used for cell-type deconvolution and cell type-specific differential expression in spatial transcriptomics.