Package index • ShennongTools

Core Functions

Main functions for tool execution and initialization

sn_options(): Get or Set ShennongTools Options

sn_run(): Run Tool Command

Tool Management

Functions for managing tools and toolboxes

sn_add_tool(): Add Tool to Toolbox

sn_diagnose_tool(): Diagnose Tool Installation

sn_initialize_toolbox(): Initialize a Toolbox

sn_install_micromamba(): Install micromamba

sn_install_tool(): Install a tool or environment

sn_remove_tool(): Remove Tool from Toolbox

sn_reset_toolbox(): Reset Default Toolbox

sn_validate_tool(): Validate Tool Configuration

Tool Information and Help

Functions for getting tool information and help

sn_get_tool_config(): Get Tool Configuration

sn_get_tool_info(): Get Tool Information

sn_help(): Get Help for Tool or Command

sn_help_builtin(): Get Help for Built-in Tool

sn_list_tools(): List Available Built-in Tools

sn_load_registry(): Load Tool Registry

sn_show_tool(): Show Tool Details

S4 Classes and Methods

S4 class definitions and their methods

Tool-class: Tool S4 Class

Toolbox-class: Toolbox S4 Class

ToolCall-class: ToolCall S4 Class

show(<Tool>): Show Method for Tool

show(<Toolbox>): Show Method for Toolbox

show(<ToolCall>): Show Method for ToolCall

Accessor Functions

Safe accessors for S4 objects

sn_get_installed_versions(): Get Installed Versions

sn_get_tool(): Get Tool from Toolbox

sn_get_tool_commands(): Get Tool Commands

sn_get_tool_name(): Get Tool Name

sn_get_tool_version(): Get Tool Default Version

sn_get_tool_versions(): Get All Tool Versions

sn_get_toolbox_tools(): Get Toolbox Tools

sn_get_toolcall_outputs(): Get ToolCall Output Files

sn_get_toolcall_runtime(): Get ToolCall Runtime

sn_get_toolcall_status(): Get ToolCall Status

sn_is_tool_installed(): Check if Tool Has Any Version Installed

sn_is_toolcall_success(): Check if ToolCall was Successful

Template System

Template rendering and testing

sn_render_python_template(): Render Python Template

sn_render_template(): Render Template with Parameters using Jinjar

sn_test_template(): Test Template Rendering

Mock Data Generation

Functions for generating mock biological data for testing

sn_cleanup_mockdata_examples(): Clean Up Mock Example Files

sn_generate_mockdata(): Generate Mock Data Files

sn_generate_mockdata_batch(): Generate Mock Data for Multiple Files

sn_generate_rnaseq_dataset(): Generate Compatible Mock Dataset for RNA-seq Analysis

sn_get_example_value_with_mockdata(): Generate Mock Example Value with Temporary File

Utilities

Utility and maintenance functions