Tool development

Developing Galaxy tools in general

In case you are not familiar with Galaxy tool development, there is plenty of supports to help you beginning and improving.

Don’t know where to start? There are very cool and easy-to-handle tutorials hosted by the Galaxy Training Network. You can also have a look at the contribution guidelines we wrote for our W4M contributors and collaborators.

Please note that W4M also hosts a GitHub repository aiming to gather tools and contributors from the metabolomics world. More information available in the associated Readme

Developing tools compatible with W4M input/output datasets

Due to the diversity of tools needed to construct comprehensive metabolomic workflows, W4M chose to adopt common standards across its tools, in particular regarding data table formats.

About the W4M standardised 3-tables format

As W4M provides a large variety of tools, we set a common way to handle data, in order to enable easy links between the tools, limiting format switches and ensuring users can easily find the information they seek inside their data sets.

For any extracted data (i.e. a single intensity value per {analytical variable; sample} pair), we settled for a standardised 3-tables format, in the form of ‘tabular’ files (as defined in Galaxy, i.e. plain text files (.txt, .tsv, .tabular) containing tables with columns separated by tabulations). One file is dedicated to the intensity values measured for each analytical variable and each sample, a second file gathers the meta-data concerning the samples, and a third file is about the meta-data of the analytical variables.

Detailed information about this W4M 3-tables format is available here.

Familiar with Biobase formating from Bioconductor? The W4M 3-tables format is very similar to the ExpressionSets organisation of data, the main difference being that the dataMatrix table is a transposition of the assay data table:

W4M format	ExpressionSets
dataMatrix	transposed assay data (assayData)
sampleMetadata	phenotypic data (phenoData)
variableMetadata	annotations and feature data (annotation)

Developing tools in a W4M-approuved format

TODO blabla intro

The tool being wrapped

TODO topo sur le user experience

TODO Ajout de la ref à W4MRUtils dans le cas de codes en R.

The Galaxy XML wrapper

Among the possible variations for functional XML wrappers, W4M is willing to garantee […]

TODO les reco W4M du XML

Documenting the Galaxy tool

Documentation in vital to any tool. Among the many advantages it provides, it enables potential users as well as already initiated ones to understand what the tool is meant for and how it can be relevantly used.

As you may already know, there are two distinct targets for documentation, that are equally important: - the developers’ community: people that may evaluate your tool in a ‘code and structure’ perspective, that may deploy it for others or themselves to use it, and that may also contribute to its development in the future - the users’ community: people that may test your tool in order to obtain results, that may use it for their routine or R&D works, and that may even use it for learning purpose.

W4M supports Galaxy tools that combine these two aspects of documentation. Consequently, we highly recommend that any tool you share with our community is provided with at least basic documentation for both these target publics.

Documentation for developers

TODO Mentionner les BP (comm etc) + dire que minimum un ReadMe mais aussi les tests pour exemple a rejouer

Documentation for users

There is a large variety of ways to provide user documentations, including embedded help files, online content and even live trainings’ supports.

As one of Galaxy’s goals is to provide a user-friendly environment and easy access to ressources, several channels exists that are especially designed to be efficient for users (easily found, convenient to use…).

As W4M, we highly recommend to consider at least the three following options.

The Galaxy tool Help section

TODO Presenter les section mandatory et facultative

About the format, you can find here a template of Help tag to help you initiating your writing with the recommanded sections and formats.

Other Galaxy tool’s XML information usefull for users

TODO les balises recommandees

Materials to provide through the Galaxy Training Network

TODO Le fait que bon moyen de mettre en ontexte un outil + Lien vers GTN et howto GTN-build + le fait que ça apparaitra direct en bas de l’outil