Conversion bruker data

[ypriverol]

• [x] added the option extension_convert reflecting discussion in https://github.com/bigbio/sdrf-pipelines/issues/145 and PR in quantms https://github.com/bigbio/quantms/pull/275.
• [x] version increased to 0.23.
• [x] minor changes to the tests.

[jpfeuffer]

Can you add a "--version" command so we dont have to hardcode the version in workflows everytime and everywhere? Would be awesome

[ypriverol]

parse_sdrf.py --version give the version of the tool.

[jpfeuffer]

How can you specify that both raw and d are converted to mzml?

[ypriverol]

You mean having a conversion where you have more than one file type? Right now you will only have one file type to another, this is allowed: d:mzML or raw:mzML, d:d, etc.

[jpfeuffer]

what if you have multiple file types in the initial design?

[ypriverol]

We don't allow that in quantms or even OpenMS. I guess is a really future use case.

[jpfeuffer]

It is allowed in quantms. I ran pipelines with raw and mzml before.

[jpfeuffer]

If you only allow one type of raw file, why a mapping at all? Then you just need an option "out_type".

[ypriverol]

Ok, what will be the expected behaviour, something like:

raw:mzml d:d

Which mean convert the raw to mzml and keep the d as d?

[jpfeuffer]

Yes exactly.

[ypriverol]

What should happen if the user gives contradictory changes, like d:d and d:raw ? Error?

[ypriverol]

I will put the following behavior: --extension_convert 'raw:mzml, d:mzml' if multiple conversion options are provided for the same filetype: raw:mzml, raw:raw the tool will through an error.

[ypriverol]

@jpfeuffer the following commit allows multiple file conversions: https://github.com/bigbio/sdrf-pipelines/pull/148/commits/9c304a7a4dac617f231c1f4f251c5fb9d506caf4