my file is in tsv format, and I cannot for the life of me find the issue, I have compared the file visually in notepad++ with the HMP2_taxonomy.tsv on the Github page, and they look identical, its UFT-8, I even did the EOL conversion from windows to Unix, but the file wont upload in the Get data function.
has anyone had a similar problem? Im happy to share my tsv file
Hum .. tricky. I would try opening the file in a very basic Unix/Linux command line editor like vim. Then toggle on all of the hidden characters to visible (there are guides online). What do you see? Make changes as needed.
In the end, you will want ^I tabs between the columns and lines that end with a newline $ and no blank lines at the end. Then save the file, Upload to Galaxy using all defaults so that the format is detected (a Galaxy “guess”). This should be then assigned as tabular and you can use it with the tool.
You could also just try loading with the “guess” to eliminate assigning the datatype directly as the problem. The tool is reporting “cvs” a lot in the error. Is the datatype set correctly? Also, make sure the file is not compressed first. But if that is not enough, fall back to the very simple plain text editor.
Moving from Windows into Linux is always a bit difficult. Worse case, get something into Galaxy and edit files with the Text Manipulation tools or directly in a super simple “notepad” type of environment with Visualization → Editor (requires some file first, but this could be data pasted into the Upload tool?).
Let us know if this was solved or not! Or maybe one of these suggestions helps?
Im trying to follow the Maaslin2 tutorial, on the Galaxy webtool, but I keep getting this error when I try to upload my abundance data file