| Previous changeset 30:14b1c52fae62 (2020-02-12) Next changeset 32:b02d1992a43a (2021-04-07) |
|
Commit message:
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40" |
|
modified:
abims_xcms_xcmsSet.xml lib.r macros_xcms.xml xcms_xcmsSet.r |
| b |
| diff -r 14b1c52fae62 -r eb15a3841da4 abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Wed Feb 12 08:30:58 2020 -0500 +++ b/abims_xcms_xcmsSet.xml Tue Apr 28 09:35:10 2020 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0"> +<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy1"> <description>Chromatographic peak detection</description> <macros> @@ -30,6 +30,7 @@ #if $methods.method == "CentWave": @COMMAND_CENTWAVE@ + peaklist $methods.CentWaveAdv.peaklist ## List of regions-of-interest (ROI) #set $sectionROI = $methods.CentWaveAdv.CentWaveAdvROI @COMMAND_CENTWAVEADVROI@ @@ -61,6 +62,7 @@ snthresh $methods.MatchedFilterAdv.snthresh steps $methods.MatchedFilterAdv.steps mzdiff $methods.MatchedFilterAdv.mzdiff + peaklist $methods.MatchedFilterAdv.peaklist #elif $methods.method == "MSW": snthresh $methods.snthresh verboseColumns $methods.verboseColumns @@ -103,6 +105,7 @@ <expand macro="input_centwave"/> <section name="CentWaveAdv" title="Advanced Options" expanded="False"> <expand macro="input_centwaveAdv"/> + <param argument="peaklist" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Get a list of found chromatographic peaks" help="Generates a tabular file with all the chromatographic peaks obtained." /> <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="False"> <expand macro="input_centwaveAdvROI" optional="true"/> </section> @@ -134,6 +137,7 @@ <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" /> <param argument="steps" type="integer" value="2" label="Number of bins to be merged before filtration" help="(i.e. the number of neighboring bins that will be joined to the slice in which filtration and peak detection will be performed)" /> <param argument="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-binSize*steps " /> + <param argument="peaklist" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Get a list of found chromatographic peaks" help="Generates a tabular file with all the chromatographic peaks obtained." /> <!-- index --> </section> </when> @@ -183,6 +187,12 @@ <outputs> <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" /> <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" /> + <data name="peaklist_out1" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > + <filter>methods['method'] == 'CentWave' and (methods['CentWaveAdv']['peaklist'])</filter> + </data> + <data name="peaklist_out2" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > + <filter>methods['method'] == 'MatchedFilter' and (methods['MatchedFilterAdv']['peaklist'])</filter> + </data> </outputs> <tests> @@ -492,6 +502,11 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +**Version 3.6.1+galaxy1 - 22/04/2020** + +- NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods. + + @HELP_XCMS_NEWVERSION_3610@ **Version 3.4.4.1 - 30/04/2019** |
| b |
| diff -r 14b1c52fae62 -r eb15a3841da4 lib.r --- a/lib.r Wed Feb 12 08:30:58 2020 -0500 +++ b/lib.r Tue Apr 28 09:35:10 2020 -0400 |
| [ |
| @@ -151,12 +151,14 @@ group_colors <- brewer.pal(length(unique(xdata$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) } |
| b |
| diff -r 14b1c52fae62 -r eb15a3841da4 macros_xcms.xml --- a/macros_xcms.xml Wed Feb 12 08:30:58 2020 -0500 +++ b/macros_xcms.xml Tue Apr 28 09:35:10 2020 -0400 |
| b |
| @@ -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" > |
| b |
| diff -r 14b1c52fae62 -r eb15a3841da4 xcms_xcmsSet.r --- a/xcms_xcmsSet.r Wed Feb 12 08:30:58 2020 -0500 +++ b/xcms_xcmsSet.r Tue Apr 28 09:35:10 2020 -0400 |
| b |
| @@ -40,6 +40,7 @@ if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum if (!is.null(args$filterRt)) filterRtParam <- args$filterRt if (!is.null(args$filterMz)) filterMzParam <- args$filterMz +if (!is.null(args$peaklist)) peaklistParam <- args$peaklist method <- args$method @@ -100,6 +101,14 @@ #chromTIC = chromatogram(xdata, aggregationFun = "sum") #chromBPI = chromatogram(xdata, aggregationFun = "max") +# Create a chromPeaks table if required +if (exists("peaklistParam")) { + if(peaklistParam){ + cat("\nCreating the chromatographic peaks' table...\n") + write.table(chromPeaks(xdata), file="chromPeak_table.tsv",sep="\t",quote=F,row.names=F) + } +} + cat("\n\n") # ----- EXPORT ----- |