# 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 @@
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.. 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.
-
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-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’)
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-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 @@
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