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Updated: Nov 25, 2025
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
aCLImatise: automated generation of tool definitions for bioinformatics workflows
Michael Milton1,2, Natalie Thorne1,2,3,4
1Melbourne Genomics Health Alliance, Parkville, VIC 3052, Australia.
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.
