Issue with Agilent Qtof files

computational-metabolomics / mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching

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Closed yguitton closed 3 years ago

yguitton commented 3 years ago

Hi Tom,

I hope your fine

I have some Agilent QTof Files to process and I was trying to use msPurity in W4M, but I face an issue in Galaxy https://workflow4metabolomics.usegalaxy.fr/u/florence/h/mediana-pos-msmsreadpuritymsp

In Rstudio I managed to process one file so may be it's more a Galaxy issue maybe linked to #41

library(msPurity)
pa<-purityA("LIPO1.mzML",offsets = c(0.65,0.65))
pa@puritydf

Any clue?

Thanks for your help Yann

yguitton commented 3 years ago

Hi Tom,

It seems that the error is linked to the minoffset parameter that is not correctly send to Galaxy

tool error
An error occurred with this dataset:
cannot find 'minoffset'

All the best Yann

Tomnl commented 3 years ago

Hi @yguitton

Sorry! This should now be fixed in the latest toolshed version of the tools.

It was actually fixed by @bernt-matthias in #41 but I didn't get round to pushing to the toolshed.

Let me know if you get any problems.

yguitton commented 3 years ago

Hi @Tomnl,

Many thanks for the tool update. I will ask to have it installed on usegalaxy.fr

Cheers Yann