Tbtools

What it does

When your agent uses it

• The user asks about TBtools
• TBtools RPC API
• Bioinformatics operations available through TBtools such as sequence manipulation
• GFF/GTF/GXF processing

Example prompts

• “/tbtools”

Requirements

• Python 3
• PowerShell

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

1. 1Create deterministic workspace folders and pass absolute host-local file paths. RPC bodies carry paths, not file content.
2. 2Call system.listMethods and system.describeMethod for candidate methods. Use system.toolsJson when many method schemas are needed.
3. 3Prefer a matching *.validateParams or *.validateInput before *.process when available.
4. 4Treat validation failures carefully: validate methods may return result.ok = false / validated = false with structured errors instead of a…
5. 5For long BLAST, tree, heatmap, NCBI, or large file jobs, raise client timeout and reduce concurrency.
6. 6If JSON-RPC error -32603 has error.data.reason = rpc pool busy, back off and retry with lower concurrency.

What it can do on your machine

Read from SKILL.md and the folder at commit 4168f80. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships 1 file in scripts/ (PowerShell), which the agent can run.

  Shell commands in SKILL.md call:

  • java
  • curl
  • python3

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md. Its commands use curl, which can reach the network depending on how they are called.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Tbtools loads about 2.3k tokens when it runs. Until then it costs about 72 tokens; SKILL.md has 488 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~72

When it runs · the whole SKILL.md, loaded when a task matches

~2.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from xuzhougeng/wispterm at commit 4168f80, republished under its MIT licence (© xuzhougeng). 488 words, ~2,331 tokens.

name

tbtools

description

Use when the user asks about TBtools, TBtools-II, TBtools RPC API, TBtools CLI, or bioinformatics operations available through TBtools such as sequence manipulation, BLAST, GFF/GTF/GXF processing, expression tables, heatmaps, trees, MCScanX, DIAMOND, HMMER, MUSCLE, and IQ-TREE.

$TbtoolsHome = if ($env:TBTOOLS_HOME) { $env:TBTOOLS_HOME } else { "C:\Program Files\TBtools" }
$TbtoolsJar = if ($env:TBTOOLS_JAR) { $env:TBTOOLS_JAR } else { Join-Path $TbtoolsHome "TBtools_JRE1.6.jar" }
$env:Path = "$(Join-Path $TbtoolsHome 'bin');$env:Path"

Test-Path $TbtoolsJar
java -version

TBTOOLS_HOME="${TBTOOLS_HOME:-/Applications/TBtools-II}"
TBTOOLS_JAR="${TBTOOLS_JAR:-$(find "$TBTOOLS_HOME" -name 'TBtools*.jar' -maxdepth 4 2>/dev/null | head -1)}"
export PATH="$TBTOOLS_HOME/bin:$PATH"

[ -f "$TBTOOLS_JAR" ] && echo "jar: $TBTOOLS_JAR" || echo "TBtools jar not found — set TBTOOLS_JAR"
java -version

blastn -query query.fa -db db_prefix -out results.tsv -outfmt 6
muscle -in input.fa -out aligned.fa
iqtree -s aligned.fa -m MFP -bb 1000 -nt AUTO
diamond blastp -d proteins.dmnd -q query.fa -o matches.tsv

.\scripts\start_rpc_server.ps1 -Background

java -cp $TbtoolsJar biocjava.rpc.RpcServer

java -cp "$TBTOOLS_JAR" biocjava.rpc.RpcServer &

function Invoke-TBtoolsRpc {
    param(
        [Parameter(Mandatory=$true)][string]$Method,
        [hashtable]$Params = @{},
        [string]$Uri = "http://127.0.0.1:8765/rpc",
        [int]$TimeoutSec = 600
    )

    $body = @{
        jsonrpc = "2.0"
        method = $Method
        params = $Params
        id = [guid]::NewGuid().ToString()
    } | ConvertTo-Json -Depth 50

    $response = Invoke-RestMethod -Method Post -Uri $Uri -ContentType "application/json" -Body $body -TimeoutSec $TimeoutSec
    if ($null -ne $response.error) {
        $reason = if ($response.error.data -and $response.error.data.reason) { " ($($response.error.data.reason))" } else { "" }
        throw "TBtools RPC error $($response.error.code): $($response.error.message)$reason"
    }
    return $response.result
}

tbtools_rpc() {
    local method="$1"
    local params="${2:-{}}"
    local uri="${TBTOOLS_RPC_URI:-http://127.0.0.1:8765/rpc}"
    curl -s --max-time 600 -X POST "$uri" \
        -H "Content-Type: application/json" \
        -d "{\"jsonrpc\":\"2.0\",\"method\":\"$method\",\"params\":$params,\"id\":\"1\"}"
}

# Windows
Invoke-WebRequest -UseBasicParsing http://127.0.0.1:8765/health
Invoke-TBtoolsRpc -Method system.ping
$methods = (Invoke-TBtoolsRpc -Method system.listMethods).methods
$methods | Where-Object { $_ -like "*Fasta*" }
Invoke-TBtoolsRpc -Method system.describeMethod -Params @{ method = "FastaStat.process" }
Invoke-TBtoolsRpc -Method system.toolsJson

# macOS / Linux
curl -s http://127.0.0.1:8765/health
tbtools_rpc system.ping
tbtools_rpc system.listMethods | python3 -c "import sys,json; [print(m) for m in json.load(sys.stdin)['result']['methods']]"
tbtools_rpc system.describeMethod '{"method":"FastaStat.process"}'

Invoke-TBtoolsRpc -Method FastaStat.process -Params @{
    inputPath = "D:/data/genome.fa"
    outputPath = "D:/data/out/genome_stat.xls"
    options = @{ getLengthOnly = $false }
}

tbtools_rpc FastaStat.process \
  '{"inputPath":"/data/genome.fa","outputPath":"/data/out/genome_stat.xls","options":{"getLengthOnly":false}}'

Invoke-TBtoolsRpc -Method AmazingFastaExtract.process -Params @{
    inputPath = "D:/data/genome.fa"
    idListPath = "D:/data/ids.txt"
    outputPath = "D:/data/out/extracted.fa"
    options = @{
        usePattern = $false
        caseInsensitive = $true
        dontTreatSpaceAsColSep = $false
        wholeWordMatch = $false
    }
}

$params = @{
    inputPath = "D:/data/sequences.fa"
    outputPath = "D:/data/out/tree"
    options = @{ ultraFastBS = $true; bbTime = 5000; model = "Auto"; threads = 2 }
}
$check = Invoke-TBtoolsRpc -Method OneStepBuildATree.validateParams -Params $params
if ($check.ok -eq $false -or $check.validated -eq $false) { $check.errors; throw "TBtools validation failed" }
Invoke-TBtoolsRpc -Method OneStepBuildATree.process -Params $params -TimeoutSec 7200

tbtools_rpc OneStepBuildATree.validateParams \
  '{"inputPath":"/data/sequences.fa","outputPath":"/data/out/tree","options":{"ultraFastBS":true,"bbTime":5000,"model":"Auto","threads":2}}'
tbtools_rpc OneStepBuildATree.process \
  '{"inputPath":"/data/sequences.fa","outputPath":"/data/out/tree","options":{"ultraFastBS":true,"bbTime":5000,"model":"Auto","threads":2}}'

© xuzhougeng, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file (scripts) in plugins/skills/tbtools of xuzhougeng/wispterm.

• SKILL.md
• scripts/start_rpc_server.ps1

Open the folder on GitHubat commit 4168f80