Sorry for the delayed response on this - I just wanted to confirm that yes Galaxy does this for uploaded files (if tools produce these line endings we would not touch those). I believe this can be disabled by clicking on the settings icon for a particular upload row in the upload form and unchecking "Use POSIX standard".
-John
On Thu, Feb 9, 2017 at 8:58 AM, Lawrence, Cris W crisl@upenn.edu wrote:
I have observed that when I upload a file with CRLF line endings into Galaxy and then later download it, the endings have changed to UNIX (LF only). I also observed that an uploaded file containing CR only line endings in Galaxy downloads to a file again with LF only line endings. These file types are txt. Just want to confirm - does Galaxy scrub line endings?
- Cris
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