Preparation for release to the stable toolshed

[Tomnl]

General

This pull requests is to make all vital updates before submitting to the Galaxy stable toolshed.

Key updates

• Name and ID changes - the tool names now reflect the R package equivelant (all tools can still be accessesed via the test-toolshed using the old IDs)

• New tools and approaches for toolshed

  • msPurity.averageFragSpectra
  • msPurity.filterFragSpectra
  • msPurity.createDatabase (uses updated schema)
  • msPurity.spectralMatching (uses updated schema and multiple matching algs)

• Format of the github repo updated

Tools for Galaxy stable toolshed

msPurity

These tools are directly from the msPurity package

Name	ID	Description
msPurity.purityA	mspurity_puritya	Assign fragmentation spectra to XCMS features using msPurity
msPurity.frag4feature	mspurity_frag4feature	Using a purityA object, filter fragmentations spectra associated with an XCMS feature
msPurity.filterFragSpectra	mspurity_filterfragspectra	Using a purityA object, link MS/MS data to XCMS features
msPurity.averageFragSpectra	mspurity_averagefragspectra	Average and filter fragmentation spectra (Inter, Intra or All)
msPurity.createDatabase	mspurity_createdatabase	Create and SQLite database of an LC-MS(/MS) experiment
msPurity.spectralMatching	mspurity_spectralmatching	Spectral matching for LC-MS/MS datasets
msPurity.combineAnnotations	mspurity_combineannotations	Combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
msPurity.createMSP	mspurity_createmsp	Using a purityA object, create an MSP file of fragmentation spectra
msPurity.dimsPredictPuritySingle	mspurity_dimspredictpuritysingle	Assess the anticipated (predicted) precursor ion purity from a DI-MS dataset
msPurity.purityX	mspurity_purityx	Assessing anticipated (predicted) purity of XCMS features from an LC-MS run
msPurity.flagRemove	mspurity_flagremove	Flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds (e.g. RSD of intensity and retention time).

Utils tools

These are helper tools that are not directly from the msPurity R package but provide useful related functionality

Name	ID	Description
track_rt_raw	track_rt_raw	Alternative approach to keep track of retention time from XCMS features
msp_split	msp_split	Split MSP file into multiple files
submit_to_mogi	submit_to_mogi	Submit data to MOGI interface and database

Associated code for each tool

Name	R
msPurity.purityA	msPurity::purityA (S4 class object)
msPurity.frag4feature	msPurity::frag4feature (class function of purityA object)
msPurity.filterFragSpectra	msPurity::filterFragSpectra (class function of purityA object)
msPurity.averageFragSpectra	msPurity::averageAllFragSpectra msPurity::averageIntraFragSpectra msPurity::averageInterFragSpectra (class functions of purityA object)
msPurity.createDatabase	msPurity::createDatabase
msPurity.spectralMatching	msPurity::spectralMatching
msPurity.combineAnnotations	msPurity::combineAnnotations
msPurity.createMSP	msPurity::createMSP
msPurity.dimsPredictPuritySingle	msPurity::dimsPredictPuritySingle
msPurity.purityX	msPurity::purityX
msPurity.flagRemove	msPurity::flag_remove
track_rt_raw	R code in Galaxy tool repository
msp_split	Python code in Galaxy tool repository
submit_to_mogi	curl command in Galaxy tool

Name, file and ID changes

New name	New ID	New Filename	Old name	Old ID	Old filename
msPurity.purityA	mspurity_puritya	purityA.xml	assess_purity_msms	assess_purity_msms	assess_purity_msms.xml
msPurity.frag4feature	mspurity_frag4feature	purityA-frag4feature.xml	frag4feature	frag4feature	frag4feature.xml
msPurity.purityX	mspurity_purityx	purityX.xml	anticipated_purity_lcms	anticipated_purity_lcms	anticipated_purity_lcms.xml
msPurity.flagRemove	mspurity_flagremove	flagRemove.xml	flag_remove_peaks	flag_remove_peaks	flag-remove-peaks.xml
msPurity.dimsPredictPuritySingle	msPurity.dimsPredictPuritySingle	dimsPredictPuritySingle.xml	anticipated_purity_dims	anticipated_purity_dims	anticipated_purity_dims.xml

New database schema and spectral matching tools

Rather than update the original database and spectral matching tools. The old tools are still available but are now deprecated (i.e. they will be available in the github repository and on test tool shed but will not be pushed to the stable toolshed)

For future analysis it is intended that the following tools should now be used in replace of create_sqlite_db and spectral_matching

Name	R	Reason for new tool
createDatabase	msPurity::createDatabase	New schema to use for the spectral-database (deprecates create_sqlite_db)
spectralMatching	msPurity::spectralMatching	New schema to use for spectral-database and update of the filtering to be more flexible (deprecates spectral_matching)

See https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html

Additional (potential) work still to do

• Update bioconda
• Ensure compatibility with XCMS 3
• Plotting of spectral matching
• Test with Brum workflow
• Test with W4M workflow

[Tomnl]

Hi both @RJMW @jsaintvanne

There are a lot of changes here - but hopefully the updates will be useful

Let me know if you want me to explain anything in more details - if you are both OK with the changes I will merge when the updated msPurity and msPurityData package are in bioconda

[jsaintvanne]

Hi,

A lot of work on this package! Good to see it ! I will try it with our workflow to see if I can run it correctly but that looks very good! Good job :)

@yguitton @lecorguille

[Tomnl]

Thanks @jsaintvanne. Let me know if you need any more information or if any bugs come up

[Tomnl]

It looks like it will be a while before bioconductor 3.9 release is in bioconda properly - potentially some time in July.

So for now, I will add the tools to the test toolshed as is, and my 'tomnl' conda channel will need to be added to the Galaxy channels if the tools are to be used.

When the Bioconda-bioconductor v3.9 is released I will push the tools to the stable toolshed

I might also merge this branch into stable - to avoid confusion for the Galaxy conference.

Any objections? @RJMW @jsaintvanne

[jsaintvanne]

Hi Thomas !

No objections for me ! We are working with your tool to be able to have our constraint with MS1 files corresponding to MS2 files ! I'm looking at this to see what is possible with zero modifications on msPurity (should be easier for everybody !). I'm working on it and we should met sometimes with @lecorguille and @yguitton to see this together :)

But your work looks very good for the moment and all looks working for me !