Hi,
I am doing metagenomics analysis for a set of samples. I want to look for mobile genetic elements (Integrons, transposons) in the reads, but am unable to find any tool for the same in Galaxy. Can someone help me with this and let me know if any tool is available?
Hello @sm9412
Please see the Metagenomics Learning Pathway at the GTN.
Toward the end is a tutorial that seems to be what you are looking for.
We are running a training later this month that will cover most of those early data preparation steps. The author’s of the tutorials will be directly available to guide you through the processing. Anyone can join and it is free! → Galaxy Training Academy 2025
Hope this helps! 
Thank you. Will check this out.