# bbav20311 Skill 契约定义
# 基于 ClawBio SKILL.md 格式

name: gene-family-plant
description: 植物学基因家族分析专业助手 - 支持11个分析阶段的标准化基因家族分析流程
version: 1.0.0
author: xialab
metadata:
  openclaw:
    requires:
      bins:
        - python3
        - conda
      env:
        - test4py311
      config: []
    always: false
    emoji: "🧬"
    homepage: https://github.com/xialab/bbav20311
    os: [linux]
    min_python: "3.11"
    install:
      - kind: conda
        environment: environment.yml
    system_dependencies:
      - hmmer>=3.4
      - blast>=2.17.0
      - mafft
      - iqtree
      - meme>=4.11.2
      - r-base>=4.4.3
      - seqkit>=2.12.0

# 分析阶段定义
stages:
  - name: identify
    description: 基因家族鉴定
    order: 1
    required: true
    inputs:
      - protein_fasta
      - hmm_file
    outputs:
      - final_members
      - identify_report

  - name: phylogeny
    description: 系统发育分析
    order: 2
    required: false
    depends_on:
      - identify
    inputs:
      - final_proteins
    outputs:
      - phylogenetic_tree
      - msa_alignment
      - phylogeny_report

  - name: motif
    description: Motif分析
    order: 3
    required: false
    depends_on:
      - identify
    inputs:
      - final_proteins
    outputs:
      - meme_xml
      - motif_report

  - name: domain
    description: Domain分析
    order: 4
    required: false
    depends_on:
      - identify
    inputs:
      - final_proteins
    outputs:
      - domtblout
      - domain_report

  - name: structure
    description: 基因结构分析
    order: 5
    required: false
    depends_on:
      - identify
      - phylogeny
    inputs:
      - gff3_file
      - final_members
    outputs:
      - structure_gff3
      - structure_report

  - name: promoter
    description: Promoter分析
    order: 6
    required: false
    depends_on:
      - identify
      - phylogeny
    inputs:
      - genome_fasta
      - gff3_file
    outputs:
      - promoter_sequences
      - promoter_report

  - name: synteny
    description: 种内共线性分析（MCScanX / Circos）
    order: 7
    required: false
    depends_on:
      - identify
    inputs:
      - genome_fasta
      - gff3_file
    outputs:
      - synteny_results
      - synteny_report

  - name: karyotype
    description: 核型分析
    order: 8
    required: false
    depends_on:
      - identify
      - synteny
    inputs:
      - genome_fasta
      - gff3_file
    outputs:
      - karyotype_plot
      - karyotype_report

  - name: interspecies
    description: 物种间共线性分析（跨物种 / JCVI-MCScan 流程，区别于种内 synteny）
    order: 9
    required: false
    depends_on:
      - identify
    inputs:
      - reference_genome
      - reference_gff3
    outputs:
      - interspecies_synteny
      - interspecies_report

  - name: combo
    description: 综合分析可视化
    order: 10
    required: false
    depends_on:
      - phylogeny
      - motif
      - domain
      - structure
    inputs:
      - tree_nwk
      - meme_xml
      - domtblout
      - structure_gff3
    outputs:
      - combo_plot
      - combo_report

# 输入文件定义
inputs:
  protein_fasta:
    type: fasta
    description: 蛋白质序列文件
    required: true
    extensions: [.fa, .fasta, .faa, .pep]

  genome_fasta:
    type: fasta
    description: 基因组序列文件
    required: false
    extensions: [.fa, .fasta, .fna]

  gff3_file:
    type: gff3
    description: 基因注释文件
    required: false
    extensions: [.gff, .gff3]

  hmm_file:
    type: hmm
    description: HMM模型文件
    required: true
    extensions: [.hmm]

  reference_fasta:
    type: fasta
    description: 参考序列文件
    required: false
    extensions: [.fa, .fasta]

  subfamily_file:
    type: tsv
    description: 亚家族分类文件
    required: false
    extensions: [.tsv, .txt]

# 输出文件定义
outputs:
  figures:
    type: image
    description: 分析结果图片
    formats: [png, pdf, svg]
    directory: final/figures/

  tables:
    type: table
    description: 数据表格
    formats: [csv, tsv, fa, nwk]
    directory: final/tables/

  reports:
    type: markdown
    description: 分析报告
    formats: [md, json]
    directory: final/reports/

  logs:
    type: text
    description: 分析日志
    formats: [log]
    directory: logs/

# 可复现性配置
reproducibility:
  enabled: true
  generate:
    - commands.sh
    - environment.yml
    - checksums.sha256
    - manifest.json
  copy_to_project: true