Hi W4M team,
I am using Galaxy pipeline and the tool xcms_fillpeaks (fillChromPeaks) for LC-HRMS dataset.
however, I was wondering why we can't choose the argument 'param', which is feasible in the xcms function. Here the choice is automatically set on " FillChromPeaksParam" but i would rather use "ChromPeakAreaParam" instead. Is that possible to implement this possibility in the Galaxy tool please?
Best regards,
Thomas
Hi @tco22
I'm not sure to fully understand your question. But to me all fillpeaks parameters can be modified, even the advanced ones (see capture below)
Can you post here the R script you are using for that step ?
Thanks
Yann
Actually
I also use this function "fillchrompeaks" so I have not any code to share, but just seeing the source code page of the function, I see another way to do it :
Just asked to know if this is possible to implement this possibility.
Best,
Thomas
Hi @tco22
Ok I see, till now we are only using FillChromPeaksParam in our code (https://github.com/workflow4metabolomics/tools-metabolomics/blob/e9183269ad5b2e8f4551f301dc736df330aa73c6/tools/xcms/xcms_fillpeaks.r#L83)
But it seems that the addition of the ChromPeakAreaParam can be added here also.
No time on my side to do that update of the wrapper, but feel free to do so by sending us a PR on github for that. Contribution to W4M evolution is more than welcome.
Best Yann
