Update tutorials to use collections instead of separate paired datasets

https://github.com/galaxyproject/tools-iuc/pull/7281 removes the option to input paired data as separate datasets, but requires a pair.

A few tutorials could need an update:

- topics/sequence-analysis/tutorials/mapping/tutorial.md
- topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md
- topics/epigenetics/tutorials/atac-seq/tutorial.md
- topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.md

Review PR 7281 first to understand the removal of separate paired-dataset inputs and the required collection format. Then inspect the four named tutorial.md files in the mapping, AMR gene detection, ATAC-seq, and super-structures tutorials. Done means all affected examples use collections and no longer rely on separate paired datasets.

Written by the indexing model from the issue text.