# HG changeset patch # User lecorguille # Date 1518514968 18000 # Node ID 5c7a7484dc5198a365639f3a46be28cbd9126776 # Parent a4d1b79479a5bbf2b71534d1babd418e1d3d18f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 diff -r a4d1b79479a5 -r 5c7a7484dc51 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Feb 13 04:42:48 2018 -0500 @@ -0,0 +1,13 @@ + +Changelog/News +-------------- + +**Version 1.0.1 - 13/02/2017** + +- IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file + + +**Version 1.0.0 - 03/02/2017** + +- NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group + diff -r a4d1b79479a5 -r 5c7a7484dc51 macros.xml --- a/macros.xml Tue Oct 24 11:46:43 2017 -0400 +++ b/macros.xml Tue Feb 13 04:42:48 2018 -0500 @@ -12,7 +12,6 @@ bioconductor-xcms - @@ -20,7 +19,7 @@ - LANG=C Rscript $__tool_directory__/xcms.r + LC_ALL=C Rscript $__tool_directory__/xcms.r @@ -117,55 +116,14 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu .. class:: infomark -**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station Biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. @@ -173,57 +131,6 @@ - - -BPCs and TICs: tabular - - | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs - | Import BPC and TIC from xcmsSet and retcor [at once] within MultiQC_ (in or outside Galaxy) to display and navigate in the graphs. - | - In MultiQC: as tool, use the Custom Content - -.. _MultiQC: http://multiqc.info/ - -BPCs and TICs: pdf [if using zip] - - | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs in pdf format. - - - - - -Get a Peak List ---------------- - -If 'true', the module generates two additional files corresponding to the peak list: -- the variable metadata file (corresponding to information about extracted ions such as mass or retention time) -- the data matrix (corresponding to related intensities) - -**decimal places for [mass or retention time] values in identifiers** - - | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. - | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. - | Theses parameters do not affect decimal places in columns other than the identifier one. - -**Reported intensity values** - - | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: - | - into: integrated area of original (raw) peak - | - maxo: maximum intensity of original (raw) peak - | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) - - - - - -xset.variableMetadata.tsv : tabular format [If Get a Peak List == Yes] - - | Table containing information about ions - Can be used in **Normalisation/Generic_filter** and **Statitics** tools. - -xset.dataMatrix.tsv : tabular format - - | Table containing ions' intensities - Can be used **Normalisation/Generic_filter** and **Statitics** tools. - - diff -r a4d1b79479a5 -r 5c7a7484dc51 test-data/sampleMetadata_missing.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata_missing.tab Tue Feb 13 04:42:48 2018 -0500 @@ -0,0 +1,5 @@ +wt16 WT +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR diff -r a4d1b79479a5 -r 5c7a7484dc51 xcms_merge.xml --- a/xcms_merge.xml Tue Oct 24 11:46:43 2017 -0400 +++ b/xcms_merge.xml Tue Feb 13 04:42:48 2018 -0500 @@ -1,4 +1,4 @@ - + Merge xcms.xcmsSet xset in one to be used by group @@ -60,6 +60,13 @@ } sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)] + + if (any(is.na(sampclass(xset)))) { + sample_missing <- rownames(phenoData(xset))[is.na(sampclass(xset))] + error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) + print(error_message) + stop(error_message) + } #end if @@ -123,6 +130,14 @@ + + + + + + + +