I ran a MrBayes analysis on usegalaxy.eu and the job seems to have completed successfully. The summary report indicates that several MrBayes output files were generated, including .run1.t, .run2.t, .pstat, .tstat, .vstat, .mstat, and especially the consensus tree file .con.
However, in my Galaxy history I can only see/download a single .txt summary file. I cannot access the actual tree files, particularly the consensus tree file needed for visualization in FigTree.
Is this expected behavior for the current MrBayes wrapper, or could this be an output/export issue? It would be very useful if the individual MrBayes output files were made available, especially for phylogenetic studies requiring the final consensus tree.
This behavior seems unexpected, but I confirmed that it reflects the tool’s current functionality rather than a technical issue with the integration on UseGalaxy.eu.
I opened a ticket requesting that more of the raw and intermediate data files be published as outputs. My request was intentionally broad, so please feel free to clarify which files would be most useful.
From what I can tell, the intermediate files are generated during the run but discarded when the job completes. To retain them in the Galaxy history, the tool wrapper would need to define those files in the output section of the tool XML.
This tool wrapper has not been updated in about ten years and is currently available only on UseGalaxy.eu, but let’s see what the developers think. There may be implementation details that make this more difficult than it initially appears.
Did I understand what you wanted correctly? Let me know!
Thank you very much for the clarification and for opening the enhancement ticket.
Yes, you understood correctly. The main output I need is the MrBayes consensus tree file, usually the `.con` file, since this is the key result required for visualization and downstream phylogenetic interpretation in tools such as FigTree.
MrBayes runs often take several hours, and since the tool already runs fully to produce the current `.txt` summary, it would be very valuable to retain the generated tree files instead of discarding them after completion. The `.txt` file is useful as a run summary, but the consensus tree is the essential output for further analysis.
If possible, the raw tree files such as `.run1.t` and `.run2.t` would also be useful, but the `.con` consensus tree would be my priority.
