Update ANGSD: implement all other methods, and update test expectations

[mertydn]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• Use of AI
  • The contribution is mostly AI generated
  • The contribution has been assisted by AI
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

This update improves the ANGSD tool. Before, it could only do one simple thing: extract .icnts.gz for contamination analysis. Now, it supports almost all major ANGSD features.

New Inputs

Users can now upload a Reference Genome, Ancestral Genome, Sites File, and Phenotype files.

Organized the tool settings into 10 sections:

• Basic BAM Filters
• Genotype Likelihoods
• Counts and Depths
• Association Studies
• Allele Frequencies
• Site Frequency Spectrum
• Genotype Calling
• Hardy-Weinberg Equilibrium
• Major/Minor Alleles
• Other (Error rates, ABBA-BABA, HaploCall, Fasta, Heteroplasmy)

New Outputs

The tool only produced an .icnts.gz file previously. The tool now generates 23 different types of files based exactly on what you select in the menu.

[mertydn]

This is not the final version from me, so there's no need to merge it immediately. I have updated the tool using a straightforward approach for now. I have a presentation during the week, so i will give it more thought and work on it further next weekend. And please i am open to your suggestions.

[SaimMomin12]

@mertydn Feel free to remove it from draft mode once its ready