aCLImatise: automated generation of tool definitions for bioinformatics workflows

SUMMARY: aCLImatise is a utility for automatically generating tool definitions compatible with bioinformatics workflow languages, by parsing command-line help output. aCLImatise also has an associated database called the aCLImatise Base Camp, which provides thousands of pre-computed tool definitions...

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Detalles Bibliográficos
Autores principales: Milton, Michael, Thorne, Natalie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8016486/
https://www.ncbi.nlm.nih.gov/pubmed/33325479
http://dx.doi.org/10.1093/bioinformatics/btaa1033
Descripción
Sumario:SUMMARY: aCLImatise is a utility for automatically generating tool definitions compatible with bioinformatics workflow languages, by parsing command-line help output. aCLImatise also has an associated database called the aCLImatise Base Camp, which provides thousands of pre-computed tool definitions. AVAILABILITY AND IMPLEMENTATION: The latest aCLImatise source code is available within a GitHub organisation, under the GPL-3.0 license: https://github.com/aCLImatise. In particular, documentation for the aCLImatise Python package is available at https://aclimatise.github.io/CliHelpParser/, and the aCLImatise Base Camp is available at https://aclimatise.github.io/BaseCamp/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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