The bug report sent in revealed that the BED dataset contained extra spaces. Problematic formatting can produce many types of tool errors, but the solution is the same – fix the formatting, then rerun tools.
Tabular datasets (including BED data) can be cleaned-up a few ways.
1. Fix the dataset formatting locally on your computer, then Upload it to Galaxy after. Do this if you plan to use the data outside of Galaxy as well. Or, fix the data in Galaxy with one of the methods below and download a copy of the format-corrected BED dataset.
2. Remove the extra spaces during Upload to Galaxy. How-to: In the Upload tool, click on the “gear” icon and check the box to “Convert spaces to tabs”. The tool merges all consecutive “whitespace” (actual spaces or tabs) into a single “tab” – which is what is wanted for proper tabular dataset formatting, including BED data. The screenshot below shows where to find the option.
Note: If you ever decide to “paste” (or type in) tabular data lines with the Upload tool, this is a good option to use to avoid formatting issues.
Warning: Use this option carefully. Example: if a dataset has header lines, converting “whitespace to tabs” will be applied to those header lines, not just the data lines. That is not always desirable as it can introduce another formatting problem.
3. Run the tool Text Manipulation > Convert delimiters to TAB on an already loaded dataset. Use the settings shown in the screenshot below. Once the job completes, the result will have the datatype “tabular” assigned. Click on the pencil icon (Edit Attributes) for the dataset to change it back to BED, and save.
General error help: Troubleshooting resources for errors or unexpected results
Support links: https://galaxyproject.org/support/#getting-inputs-right