Mercurial > repos > lecorguille > xcms_xcmsset
diff xcms_xcmsSet.r @ 37:9ada611dd63f draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
| author | lecorguille |
|---|---|
| date | Fri, 31 Aug 2018 08:59:03 -0400 |
| parents | d39b9aff9cf7 |
| children | e8d7395a70b2 |
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--- a/xcms_xcmsSet.r Thu Apr 05 18:05:45 2018 -0400 +++ b/xcms_xcmsSet.r Fri Aug 31 08:59:03 2018 -0400 @@ -83,6 +83,10 @@ if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2]) if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam) if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam) +#Apply this filter only if file contain MS and MSn +if(length(unique(msLevel(raw_data)))!= 1){ + raw_data <- filterMsLevel(raw_data,msLevel=1) +} cat("\t\t\tChromatographic peak detection\n") # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...