skill:
  name: ppi
  version: "1.0.0"
  description: "Protein-Protein Interaction Analysis based on STRING database"
  author: "bbav20311"
  
input:
  required:
    - gene_ids: "Gene ID list file (one per line)"
    - species: "Snapshot-verified STRING TaxID, or a compatible legacy species code"
  optional:
    - normalization_species_label: "Local species label used only for gene-ID normalization; never the STRING TaxID"
    - score: 200
    - network_type: "functional"

output:
  files:
    - "{prefix}.ppi_network.tsv"
    - "{prefix}.ppi_report.md"
    - "{prefix}.ppi.manifest.json"
    - "{prefix}_id_resolution.tsv"
  optional_files:
    - "{prefix}.ppi_network.pdf"
    - "{prefix}.ppi_network.png"
    - "{prefix}.ppi_network.string.png"

environment:
  conda: "test4py311"
  
tools:
  - Python requests
  - R (igraph, ggplot2; optional local plots)
  - STRING API