Using bio.tools to generate and annotate workbench tool descriptions.

Kenzo-Hugo Hillion,Hervé Ménager,Jon Ison,Hedi Peterson,Anton Khodak,Ivan Kuzmin,Michael Crusoe,Eric Rasche

doi:10.12688/f1000research.12974.1

Abstract

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 A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation.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.

Highlights

Over the last few years, bioinformatics has played a major role in the field of biology, raising the issue of best practices in software development for the members of the bioinformatics community[1,2,3]
Generation of a tool description from a bio.tools entry Here we illustrate the generation of a tool description with the example of IntegronFinder[24], an analysis tool dedicated to the identification of integrons in bacterial genomes
Launching ToolDog in “generation mode” on the IntegronFinder entry in the bio.tools registry allows the generation of a significant portion of the tool description (Figure 4), either in Common Workflow Language (CWL) or Galaxy format

Summary

Introduction

Over the last few years, bioinformatics has played a major role in the field of biology, raising the issue of best practices in software development for the members of the bioinformatics community[1,2,3]. These practices include facilitating the discovery, deployment, and usage of tools, and several helpful solutions are available. Distribution systems are available[9,10,11,12,13] that let users locally install the tools that they need in convenient, portable and reproducible ways. The Common Workflow Language[18] (CWL) is a recent project that defines a standardized and portable tool and workflow description format, usable across different platforms

Methods

Results

Discussion

Conclusion