Using bio.tools to generate and annotate workbench tool descriptions.
Using bio.tools to generate and annotate workbench tool descriptions.
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DOI：
10.12688/f1000research.12974.1
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发表时间：
2017-01-01
期刊：
影响因子：
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通讯作者：
Menager, Herve
中科院分区：
文献类型：
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作者：
Hillion, Kenzo-Hugo;Kuzmin, Ivan;Menager, Herve
工作台和工作流系统，如Galaxy、Taverna、Chipster或基于通用工作流语言（CWL）的框架，以用户友好、可扩展和可复制的方式促进对生物信息学工具的访问。然而，在这样的环境中集成工具仍然是一个繁琐、耗时且容易出错的过程。一个主要的后果是工具的描述不完整或过时，这些描述常常缺少重要的信息，包括参数和元数据，例如文档的发布或链接。ToolDog（工具描述生成器）简化了工具的集成-这些工具已在ELIXIR工具注册表（https://bio）中注册。工具)-通过生成工具描述模板导入工作台环境。ToolDog包括两个模块。第一个模块使用特定语言的插件分析生物信息学软件的源代码，并生成用于Galaxy XML或CWL工具描述的框架。第二个模块专门使用bio.tools提供的元数据来丰富生成的工具描述。最后一个模块还可以单独使用，以完成或纠正缺少元数据的现有工具描述。
Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.