I am in usegalaxy.org and I want to merge 4 assembled transcript gtf files created using cufflinks using cuffmerge. I am unable to populate entries in the "additional GTF inputs" list. These are all GTF files that have valid contents run using cufflinks (all on usegalaxy.org). I have the correct 4 "assembled transcripts" files available for the tool that all show up nicely in the first drop down when I choose "multiple datasets" , but nothing will show up in the "repeat" dropdowns. It says "no gtf dataset collection available" in each drop down for each addition gtf input I put in. I've refreshed the page, re logged in, redid all my cufflinks assemblies...... tried safari and chrome browsers (on macbook pro).... nothing i do allows me to populate any of these valid files. Any help would be greatly appreciated.
Instead of using the second input option (multiple datasets), use the first (single datasets), with this tool. This will avoid all being selected in the first choice. With this tool, the proper input is to add in each individually so that the tools runs on all inputs together.
Hopefully you have discovered this already, or this helps! Jen, Galaxy team