The GTN tutorial for using CellProfiler in Galaxy outlines a complex workflow where each module of the pipeline is treated as a separate Galaxy tool. However, there's a more straightforward approach. Instead of manually adding each module as a tool, the entire CellProfiler pipeline can be uploaded directly to the Galaxy History and run it as a single executable tool, as described here.
Things to be done:
The GTN tutorial for using CellProfiler in Galaxy outlines a complex workflow where each module of the pipeline is treated as a separate Galaxy tool. However, there's a more straightforward approach. Instead of manually adding each module as a tool, the entire CellProfiler pipeline can be uploaded directly to the Galaxy History and run it as a single executable tool, as described here.
Things to be done: