Hi everyone, i am using cancer galaxy to analyse microbial data in QIIME2. I need to upload a metadata file in the form of a TSV file and it isn’t recognising it for some reason. I can’t view the data or use it in my next step. It also says that it cannot count lines in the dataset. I know it is saved as a TSV file so the format is correct. Can anyone recommend anything?
Hi! In the message on the input parameter you can see that the tool requires an input of datatype “tabular” or “qiime2.tabular”, and the dataset in your history has a datatype of “tsv” set. You can change the datatype on your input data to “tabular” as follows: Changing the datatype
In general, most tools use the “tabular” datatype for column-based files (regardless of separator), so I would recommend always using that in Galaxy over “tsv”
Hi shilteman, thank you for your help/ I did change it to tabular and it came up with an error. I am not sure why it does this. I have tried tsv, tabular and txt.
Easiest way for me to import a samplemetadata is to copy paste it in Galaxy upload data and it should save it as tabular or tsv format
It’s hard to know what the error is about without seeing your history, but it’s not always a problem. If you are sure your data is in the correct format for the tool you can sometimes ignore it. If it’s set to tabular it should be selectable in the tool now. (PS you can also always drag datasets from your history to the tool parameter input if it’s not shown as an option in the dropdown, but it’s better to set the correct datatype of course)
Hi Jsaintvane, That worked thank you. Do you know how to create a QIIME2 artifact with these using the qiime2 tools import? I have my paired end sequences ready (called Archaea nano practice) , my metadata and my qiime2 metadata tabulated qsv file but I am not sure how to use the import tool in Galaxy. Usually i would have a manifest file for the actual qiime2.
Happy that worked ! I’m sorry but I’m metabolomic guy so never used these kind of tools ! Just work with sampleMetadata files and I know that can be hard sometimes with these TSV files
Xref: Import qiime2 artefacts?