To date I have tried running msconvert in Galaxy EU for AB Sciex raw data format, uploaded as composite data set, with no success, I don’t know what else to try, I keep getting the following error:
msconvert] no files found matching “Composite Dataset”
[msconvert] No files specified
I used desktop version of msconvert, but the files I get are very large (blown up to ~30 GB), which makes a serious analysis very difficult.
Is this kind of bahavior normal?
This tool is covered in several tutorials. Maybe those examples will help? Find the link at the bottom of the tool form, also here https://training.galaxyproject.org/training-material/by-tool/galaxyp/msconvert.html
You could even try with the tutorial data to learn how the processing works. Upload the starting data, then import the workflow, and run it in a batch (less tedious for a quick check). Creates a sort of reference history to use as a guide.
If that also fails, or just your data fails using those same steps, would you like to share some screenshot of what those files look like, and how you are uploading them? We might be able to spot what is going on.
None of the tutorials uses composite dataset, which is what should be used for .wiff format conversion. I uploaded dataset from Pride FTP server (upload/Composite/ format=.wiff, paste links to source files in corresponding windows)
This is the link to history: