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ACLImatise: Automated generation of tool definitions for bioinformatics workflows.

ABSTRACT: 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. 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 data are available at Bioinformatics online.

SUBMITTER: Milton M

PROVIDER: S-EPMC8016486 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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aCLImatise: automated generation of tool definitions for bioinformatics workflows.

Milton Michael M Thorne Natalie N

Bioinformatics (Oxford, England) 20210401 22-23

<h4>Summary</h4>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.<h4>Availability and implementation</h4>The latest aCLImatise source code is available within a GitHub organisation, under the GPL-3.0 license: https://github.com/aCLImatise. In particular, do ...[more]

PMID: 33325479

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