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computational-metabolomics / mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching
GNU General Public License v3.0
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msPurity spectralMatching issue when polarity filter is on #44

Open yguitton opened 3 years ago

yguitton commented 3 years ago

Hi @Tomnl ,

Today, I faced an issue with the spectralMatching tool under W4M. In fact, I think that the polarity filter option is in cause as everything work fine when i juste remove that filter....

Loading required package: Rcpp
Running msPurity spectral matching function for LC-MS(/MS) data
Filter query dataset
Filter library dataset
Error: row value misused
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted

Do you have a clue?

I have open an issue on our IFB forum, to keep track of the problem. https://community.france-bioinformatique.fr/t/msms-spectralmatching-issue/855?u=yguitton

All the best

Tomnl commented 3 years ago

Hi @yguitton,

Are you able to share the history so I can check?

You are correct - I think there is a bug on the polarity filter

yguitton commented 3 years ago

Hi @Tomnl

the link https://usegalaxy.fr/u/yguitton44/h/xprocessor-test-msms dataset 245 with error

dataset 246 ok (but no polarity filter)

Thanks for your help

Tomnl commented 3 years ago

The error is when a user selects more one option selected for the polarity.

Will work fine if you use just select 'positive' or just 'negative' see https://usegalaxy.fr/u/tomnl/h/imported-miniporcblatpos-msms

I will look into making the fix.

Thanks for spotting it Tom