Update tools/freyja to 1.5.2

[SaimMomin12]

This PR updates the freyja tool to 1.5.2 and adds new --pathogen option.

Fixes: #6513

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FOR CONTRIBUTOR:

• [x] I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• [x] License permits unrestricted use (educational + commercial)
• [ ] This PR adds a new tool or tool collection
• [x] This PR updates an existing tool or tool collection
• [ ] This PR does something else (explain below)