Mercurial > repos > lecorguille > xcms_retcor
changeset 23:faf4a6b67304 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
| author | workflow4metabolomics |
|---|---|
| date | Thu, 13 Feb 2020 06:43:08 -0500 |
| parents | 972e76582173 |
| children | c8011370e90f |
| files | README.rst abims_xcms_retcor.xml xcms_retcor.r |
| diffstat | 3 files changed, 18 insertions(+), 1 deletions(-) [+] |
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--- a/README.rst Wed Feb 12 08:30:30 2020 -0500 +++ b/README.rst Thu Feb 13 06:43:08 2020 -0500 @@ -4,6 +4,10 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +**Version 3.6.1+galaxy1 - 13/02/2020** + +- NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments. + **Version 3.6.1.0 - 03/09/2019** - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
--- a/abims_xcms_retcor.xml Wed Feb 12 08:30:30 2020 -0500 +++ b/abims_xcms_retcor.xml Thu Feb 13 06:43:08 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy0"> +<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy1"> <description>Retention Time Correction</description> @@ -290,6 +290,9 @@ .. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2 .. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html +WARNING: if a retention time ajustment have already been applied to your data. +The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments. + @HELP_XCMS_MANUAL@ ------------ @@ -308,6 +311,10 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +**Version 3.6.1+galaxy1 - 13/02/2020** + +- NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments. + @HELP_XCMS_NEWVERSION_3610@ **Version 3.4.4.1 - 30/04/2019**
--- a/xcms_retcor.r Wed Feb 12 08:30:30 2020 -0500 +++ b/xcms_retcor.r Thu Feb 13 06:43:08 2020 -0500 @@ -63,6 +63,12 @@ adjustRtimeParam <- do.call(paste0(method,"Param"), args) print(adjustRtimeParam) + +if (hasAdjustedRtime(xdata)) { + cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment") + cat("Replace raw retention times with adjusted retention times.\n") + xdata <- applyAdjustedRtime(xdata) +} xdata <- adjustRtime(xdata, param=adjustRtimeParam) #cat("\t\t\tCompute and Store TIC and BPI\n")