Integrate the OpenSWATH into Galaxy

[bgruening]

More informations here:

• http://www.openswath.org/example_OpenSWATH.zip
• http://www.openswath.org/openswath_instructions.html

Programs needed:

• xinteract (TPP)
• spectrast (TPP)
• spectrast2spectrast_irt.py
• spectrast2tsv.py
• ConvertTSVToTraML*
• OpenSwathDecoyGenerator*
• OpenSWATHWorkflow*
• pyprophet
• feature_alignment.py

*All OpenMS tools can be generated automatically, the wrapper quality varies

[jmchilton]

The TPP tools are so hard to wrap since they create files with so many references embedded right in the file - which is not compatible with the way Galaxy stores files or handles outputs. It might be worth wrapping large portions of the workflow into a single tool for this reason.

[bgruening]

I hope that @iracooke awesome protk library can help here. Otherwise we can fallback to one single wrapper.
Many of these tools are also integrated in OpenMS, or this is wip. So we do not need to take care of the links at some point.

[trevor]

In the list, should that be "spectrast (PP) (TPP)"?

It looks like it's listed twice, is the second one from another source?

[bgruening]

@trevor I hope you can also edit the list above. It was listed twice because it is used twice in the workflow. I corrected this mistake. Thanks.

[sparker43]

A few additional tools that are pretty integral to the workflow:
pyprophet https://github.com/uweschmitt/pyprophet and a feature_alignment.py script (written by Hannes et al at ETH) to combine and align results files within a single experiment (https://code.google.com/p/msproteomicstools/source/browse/trunk/analysis/alignment/feature_alignment.py).

[bgruening]

Thanks @sparker43 I added it to the list.

[bgruening]

added ConvertTSVToTraML and OpenSWATHWorkflow in bgruening/galaxytools@68b57f3

[bgruening]

I will start to work on the missing tools here: https://github.com/galaxyproteomics/tools-galaxyp/tree/msproteomicstools
Contributions welcome!

[bgruening]

Inittial wrappers for pyprophet and feature_alignment are included. Does anyone have small test files?

[iracooke]

I suggest we narrow the scope of the xinteract tool since xinteract is basically just a wrapper for other tools (various Prophets, libra, asapratio etc).

Is the required functionality covered by protk tpp prophets tools?

https://github.com/iracooke/protk-galaxytools/tree/master/tpp-prophets

[bgruening]

xinteract is not needed anymore, @iracooke has the missing functionality already in protk