Hello, after running PLINK it produces output files bed, bim, fam, and log. However, when viewing these files in the History they appear as html, tab, txt, and txt files respectively. When looking at the Details→ Dataset Information of the bed file for example, it says format: pbed; and Originally created from a file named: plink_output.bed.
When I try downloading these files they also download as html, tab, and text; and so I’m unable to use them for downstream analyses. Does anyone know where the original files (plink_output.bed, plink_output.bim, plink_output.fam) might be located in Galaxy or how to retrieve or download them?
The datatypes with this tool are handled a bit differently from tools with the common shared datatypes. The developer is working to add the custom types to our registry but I think that is still a request as far as I know (no tickets against Galaxy are open yet).
Downloading PLINK data → First, download the file from Galaxy. Next, you can adjust the file extensions directly. This will allow tools outside of the Galaxy ecosystem, that would normally use the data, to recognize it. This works for any exotic file type that is not (yet) handled by Galaxy itself.
Example: This is similar to a README.md file you may download from somewhere – it needs to have the .txt extension added in before a word processing tool will understand that it is a “text file”.
Please give this a try and let us know if it works for you!
When adjusting the file extensions directly, for some reason this only worked on the bim file. However, I was able to change to adjust the file type through R program by using ‘file.rename’ function.
Glad you were able to get this to work and the need to user R is interesting. Thanks for posting the details back here for anyone else later on who needs to do this!
