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elixir-proteomics-community / sdrf_convert

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Going from parameter files to SDRF files #14

Open enryH opened 11 months ago

enryH commented 11 months ago

Hey,

so just to be sure and document it here. Veit mentioned this project to us for potential use in ProteoBench. We aim to parse parameter files into a common format (or at least parts of it).

Currently there is no way to create an SDRF files with all possible information which can be added to SDRF based on search engine parameter file, e.g. mqpar.xml from MaxQuant.

Reference: https://github.com/Proteobench/ProteoBench/issues/58

di-hardt commented 11 months ago

Great idea and simple enough. I will define a AbstractConfigConverter as it already exists for the other way around (SDRF -> Config).
Do you already have some validation or something in mind which is ture for multiple configs?

julianu commented 10 months ago

As just discuessed in the call: To adjust our work a bit, we could/shoudl take the information from this file https://github.com/bigbio/sdrf-pipelines/blob/master/sdrf_pipelines/sdrf_merge/param2sdrf.yml and make it usable as input file for the sdrf_convert (and the other way around). My idea would be to use the same naming of the parameters in the CLI (at least as an alias to the searchengine-specifc naming), but also maybe make a call possible which picks up a configured yaml file instead of typing everything into the CLI.

What do you think?