I want to use some proteomics tools but I can not find those tools like XTandem, MSGFPlus, comet, and PGNexus, etc. Please help me
Are you using a public server?
The only solution that comes to mind is:
You can install tools into Galaxy only if you are admin. So you can have your own local Galaxy and become admin. From there on you have total control of the tools there. Look for the them in the Galaxy Tool Shed (https://toolshed.g2.bx.psu.edu/). I think I have seen XTandem.
Thank you Sammy