ToolDog

ToolDog (TOOL DescriptiOn Generator) aims to generate XML template for Galaxy or CWL from the description of tools from Bio.tools.

Quick-start guide

Installation

Requirements

You need Docker to be installed on your computer in order to perform the code analysis step of ToolDog.

You can then install ToolDog using pip with the following command:

pip3 install tooldog

How does it work ?

ToolDog supports import either from bio.tools or from a local file (downloaded from bio.tools in JSON format). It can generates XML for Galaxy and CWL tool but also annotates existing ones (only support XML so far...).

usage: tooldog [-h] [-g/--galaxy] [-c/--cwl] [-f OUTFILE] biotool_entry

To import from bio.tools, specify the biotool_entry with its id or by specifying the version with the following format: id/version:

tooldog --galaxy integron_finder > integron_finder.xml

You can also use local file downloaded from bio.tools API by giving its name directly:

tooldog --galaxy integron_finder.json > integron_finder.xml

More information about ToolDog usage here.

References

Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson2, Jon Ison, Hervé Ménager. Using bio.tools to generate and annotate workbench tool descriptions [version 1; referees: 2 approved]. F1000Research 2017, 6(ELIXIR):2074 doi: 10.12688/f1000research.12974.1

Kenzo-Hugo Hillion, Jon Ison and Hervé Ménager. ToolDog – generating tool descriptors from the ELIXIR tool registry. F1000Research 2017, 6:767 (poster at ELIXIR all hands meeting). doi: 10.7490/f1000research.1114125.1

Hervé Ménager, Matúš Kalaš, Kristoffer Rapacki and Jon Ison. Using registries to integrate bioinformatics tools and services into workbench environments. International Journal on Software Tools for Technology Transfer (2016) doi: 10.1007/s10009-015-0392-z

padilha / ToolDog