Background: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs, but their potential is underutilized: web interfaces for command-line tools rarely take advantage of the level of interactivity expected of modern web applications and are rarely usable offline.Results: Here we present Pline: a lightweight framework that uses program descriptions and web standards to generate dynamic GUIs for command-line programs. We introduce a plugin system for creating Pline interfaces and provide an online repository for sharing third-party plugins. We demonstrate Pline’s versatility with example interfaces, a graphical pipeline for sequence analysis and integration to Wasabi web application.Conclusions: Pline is cross-platform, open-source software that can be integrated to web pages or used as a standalone desktop application. Pline provides graphical interfaces that are easy to create and maintain, fostering user-friendly software in science. Documentation, demo website, example plugins and source code is freely available from http://wasabiapp.org/pline. Keywords: Bioinformatics; Software Engineering; User Interfaces; Web Technologies