Hi @jennaj,
On Galaxy Europe there is a new interactive tool called physicell studio.
Here:
This is agent-based modeling software that we usually run local or on hpc.
For downstream analysis for physicell output, there exists a pip installable python package called physicell data loader (pcdl). All pcdl does is to transform physicell output into common data formats, most of the used by bioinformaticians for downstream analysis. Namely, h5ad, csv, json, gml (for graphs), txt, jpeg, tiff, png, ome.tiff, vtp and vtr (for 3d graphics). My aim was, to port pcdl (more exactly, the about 20 command line commands pcdl provides) to galaxy. So, it will be my tool that produces those files, and if there are no tools on galaxy to process them, then simply to download and process them locally.
On the big 3 (windows, mac, linux) pcdl is super easy to install and works flawless. So, I thought it will be a piece of cake to port pcdl to Galaxy ~ and frankly, I was totally proven wrong.
Anyhow, I understand now that I have to modify the filename.ext to filename.ext.galaxyext and will do so.
At this moment, I don’t plan to implement tools for galaxy to process the file types that galaxy as of today is unfamiliar with (gml and most probably vtr). I leave this to other folks in the empire : ).
Thank you for your explanation! It is now clear to me what I have to do.
This should get me a step further to finalize the pcdl galaxy port.
Best wishes, bb-8