Are the SNPs in VCF format? The tools in the group NGS: VCF Manipulation can be used to summarize (count), filter on alleles, modify the formatting to be in a tabular format (aka "Tab-delimited") and many other operations.
VCF data is more useful in coordinate sorted format, not allele frequency when used with downstream tools, so there is no specific tool for that, however, those counts output in tabular format can be sorted with Filter and Sort > Sort data in ascending or descending order and used any way you want for custom queries/manipulations.
If this does not help, please explain your starting input format/source in more detail.
Galaxy tutorials, including the 101 that includes some basic text manipulation operations: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team