Format Issue with Advance cut tool: Resolved: server side open issue 2023-09-11

Hi Galaxy community,

I have been using the Advance cut tool for several of my pipelines and recently I just notice a behavior I haven’t seen before. Basically, I use the Advance cut tool to remove unwanted columns from .pslx files with the following format:

The advance cut tool used to create as an output a tabular file with the columns I instructed to keep but recently, the tool its outputting all the values in a single column:

I have made sure my initial input file is tab delimited. Actually, I have tested with input files that were successfully processed by the tool and now is not working as before. Any ideas what might be happening?




The metadata issue from yesterday is resolved. The output was always present just not displayed correctly in the applications. Meaning, the “eye” icon will display the file output but the other metadata wasn’t updated in the history view.

If anyone ended up with a file that has strange metadata (no datatype, no line counts), do one of these:

  1. Click on the pencil icon to reach the Edit Attributes forms, and re-detect the datatype.
  2. Or, you can just rerun the job.

@xchelriv For your specific problem, my guess is that the file has some whitespace characters that are interfering with the column selections (specifically, the delimiter interpretation). I know that worked fine in a prior run, and can reproduce your results, but would still recommend cleaning up files first whenever using output from Excel, or really any spreadsheet program. Your two examples ran on the same cluster but different nodes … everything else is the same. The best guess is that at some very low level that made a difference, and points back to starting with “clean” data for best results/predictability.

So, please try this:

  1. Output tabular data from the upstream program, and upload that to Galaxy.
  2. Run the tool Convert delimiters to TAB on the file first to attempt to clean up any remaining whitespace problems.
  3. Note: there are all sorts of cases where this will not be enough. If some variables have internal whitespace, you could try outputting and uploading comma separated output (csv) instead … just be aware that other tools may complain about internal whitespace!

The default options are usually best, and should be set up like this.

tool → Convert delimiters to TAB
convert all → Whitespace
strip leading/trailing → Yes
condense → Yes

Thanks @xchelriv for posting publicly!

There is a brand new server issue at We are still working out exactly what and why.

Seems to be impacting text manipulation tools (only) so far.

We’ll post updates here. I’m going to rename your topic so others can find & follow along.

How presents:

  1. Some tabular data operation fails
  2. Empty “green” result, with no bug report available
  3. May output something (or did originally) but reruns will fail like item 2