[xcms process history] error about tools-metabolomics

[melpetera]

These two errors are fixed by #182 from @lecorguille

However, in the CAMERA case (only), an other error occurs:

Error: object 'sampleNamesList' not found
Execution halted

An example can be found in same history:
https://galaxy.workflow4metabolomics.org/u/mpetera/h/gtnlcmspreprocessing
Dataset 78

[melpetera]

It seems that in the /xcms_summary/xcms_summary.r files, sampleNamesList definition would also be needed for the case where only "xa" exists.

I am not too familiar with these different objects. I would suggest to simply turn line 76 if (exists("xa")) xobject <- xa@xcmsSet into something like the following:

if (exists("xa")) {
xobject <- xa@xcmsSet
if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xa@whatever_is_the_correct_way_to_get_the_info))
}

following what has been changed previously, but it is kind of random guess.
Maybe @lecorguille you can have a look?

[melpetera]

Handled in 9965bbc