| Previous changeset 24:761913919c21 (2020-02-12) Next changeset 26:0d05d0458376 (2020-07-21) |
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Commit message:
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40" |
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modified:
abims_xcms_group.xml lib.r macros_xcms.xml |
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| diff -r 761913919c21 -r a066b8581b97 abims_xcms_group.xml --- a/abims_xcms_group.xml Wed Feb 12 08:29:15 2020 -0500 +++ b/abims_xcms_group.xml Tue Apr 28 09:34:27 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy0"> +<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy1"> <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description> @@ -357,6 +357,10 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +**Version 3.6.1+galaxy1 - 22/04/2020** + +- BUGFIX: sample group colours were not displayed in plots. + @HELP_XCMS_NEWVERSION_3610@ @HELP_XCMS_NEWVERSION_3440@ |
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| diff -r 761913919c21 -r a066b8581b97 lib.r --- a/lib.r Wed Feb 12 08:29:15 2020 -0500 +++ b/lib.r Tue Apr 28 09:34:27 2020 -0400 |
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| @@ -151,12 +151,14 @@ group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") names(group_colors) <- unique(xdata$sample_group) + col_per_samp <- as.character(xdata$sample_group) + for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]} xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) for (i in 1:nrow(featureDefinitions(xdata))) { mzmin = featureDefinitions(xdata)[i,]$mzmin mzmax = featureDefinitions(xdata)[i,]$mzmax - plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) + plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) } |
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| diff -r 761913919c21 -r a066b8581b97 macros_xcms.xml --- a/macros_xcms.xml Wed Feb 12 08:29:15 2020 -0500 +++ b/macros_xcms.xml Tue Apr 28 09:34:27 2020 -0400 |
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| @@ -98,7 +98,7 @@ <option value="maxo">maxo</option> <option value="intb">intb</option> </param> - <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/> + <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/> </xml> <xml name="input_peaklist_section"> @@ -193,7 +193,7 @@ <option value="wMean">intensity weighted mean of the peak's m/z values</option> <option value="mean">mean of the peak's m/z values</option> <option value="apex">use the m/z value at the peak apex</option> - <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option> + <option value="wMeanApex3">intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option> <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option> </param> <param argument="integrate" type="select" label="Integration method" > |