Thank you for reporting your issue. It seems to me there is something wrong somewhere… First, on the process radtags tool (-> maybe it can be of interest for us to know if are you using the last version of the tool ? / in which Galaxy instance ?) , if you have paired-end data, you need to select as input, R1 file(s) (or collection) in the first “paired-end reads infile(s)” ““box”” and R2 file(s) (or collection) in the second “paired-end reads infile(s)” ““box””. So here, it seems to me you created a collection with both R1 and R2 files, so it’s a good dataset pair ;), but with this tool, you need to use separately R1 and R2. After saying that, normaly this tools is not “looking” at the name or content of the files when you are “just” selecting it… so… normally, if the datasets formats are ok, the tool will display these datasets on the “select box”… One exaplanation for ma can be that there is an issue using fastqsanger.gz WHEN in a collection… so MAYBE, you need to use Fastqsanger or fastqsanger.gz input files (so not in a collection) OR use fastqsanger files if in a collection… I have to test it!
So, please, can you try to “just” select your fastqsanger.gz from your history (not in collection) ? And please, pay attention to the fact that your files need to be named something like"name_R1_001.fastq" and “name_R2_001.fastq” so the execution of the tool can work
Additionally, don’t hesitate to share your history so I can have a look.