tools:
  hmmsearch:
    id: "hmmsearch"
    name: "HMMER hmmsearch"
    category: "identification"
    executable: "hmmsearch"
    docker_image: "biocontainers/hmmer:v3.3.2_cv1"
    inputs:
      - name: "query"
        type: "hmm"
        required: true
      - name: "target"
        type: "fasta"
        required: true
    outputs:
      - name: "tblout"
        type: "tblout"
      - name: "domtblout"
        type: "domtblout"
    parameters:
      e_value:
        type: "float"
        default: 1e-5
        min: 1e-100
        max: 1.0
      coverage:
        type: "float"
        default: 0.5
        min: 0.1
        max: 1.0
      cpu:
        type: "int"
        default: 4
    timeout: 7200

  blastp:
    id: "blastp"
    name: "BLASTP"
    category: "identification"
    executable: "blastp"
    docker_image: "biocontainers/blast:v2.13.0_cv1"
    inputs:
      - name: "query"
        type: "fasta"
        required: true
      - name: "db"
        type: "blastdb"
        required: true
    outputs:
      - name: "results"
        type: "blast_out"
    parameters:
      e_value:
        type: "float"
        default: 1e-5
      max_target_seqs:
        type: "int"
        default: 500
      outfmt:
        type: "int"
        default: 6
    timeout: 3600

  mafft:
    id: "mafft"
    name: "MAFFT"
    category: "alignment"
    executable: "mafft"
    inputs:
      - name: "sequences"
        type: "fasta"
        required: true
    outputs:
      - name: "alignment"
        type: "fasta"
    parameters:
      strategy:
        type: "enum"
        default: "auto"
        values: ["auto", "linsi", "ginsi", "einsi", "fftns"]
      maxiterate:
        type: "int"
        default: 1000
    timeout: 7200

  iqtree:
    id: "iqtree"
    name: "IQ-TREE"
    category: "phylogeny"
    executable: "iqtree2"
    docker_image: "biocontainers/iqtree:v2.2.0_cv1"
    inputs:
      - name: "alignment"
        type: "fasta"
        required: true
    outputs:
      - name: "tree"
        type: "newick"
      - name: "log"
        type: "log"
    parameters:
      model:
        type: "enum"
        default: "MFP"
        values: ["MFP", "LG", "WAG", "JTT"]
      bootstrap:
        type: "int"
        default: 1000
      threads:
        type: "int"
        default: 4
    timeout: 14400

  mcscanx:
    id: "mcscanx"
    name: "MCScanX"
    category: "comparative"
    executable: "MCScanX"
    inputs:
      - name: "gff"
        type: "gff"
        required: true
      - name: "blast"
        type: "blast_out"
        required: true
    outputs:
      - name: "collinearity"
        type: "collinearity"
      - name: "tandem"
        type: "tandem"
    parameters:
      match_score:
        type: "int"
        default: 50
      gap_penalty:
        type: "int"
        default: -1
    timeout: 3600

  meme:
    id: "meme"
    name: "MEME"
    category: "annotation"
    executable: "meme"
    docker_image: "biocontainers/meme:v5.0.0_cv1"
    inputs:
      - name: "sequences"
        type: "fasta"
        required: true
    outputs:
      - name: "motifs"
        type: "xml"
    parameters:
      nmotifs:
        type: "int"
        default: 10
      min_width:
        type: "int"
        default: 6
      max_width:
        type: "int"
        default: 200
    timeout: 7200

categories:
  identification:
    name: "Gene Identification"
    tools: ["hmmsearch", "blastp"]
  alignment:
    name: "Sequence Alignment"
    tools: ["mafft"]
  phylogeny:
    name: "Phylogenetic Analysis"
    tools: ["iqtree"]
  comparative:
    name: "Comparative Genomics"
    tools: ["mcscanx"]
  annotation:
    name: "Functional Annotation"
    tools: ["meme"]