Mercurial > repos > lecorguille > xcms_merge
changeset 6:5c7a7484dc51 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
| author | lecorguille |
|---|---|
| date | Tue, 13 Feb 2018 04:42:48 -0500 |
| parents | a4d1b79479a5 |
| children | dca722aecb67 |
| files | README.rst macros.xml test-data/sampleMetadata_missing.tab xcms_merge.xml |
| diffstat | 4 files changed, 41 insertions(+), 96 deletions(-) [+] |
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--- /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 +
--- 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 @@ <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> </requirements> </xml> - <xml name="stdio"> <stdio> <exit_code range="1" level="fatal" /> @@ -20,7 +19,7 @@ </xml> <token name="@COMMAND_XCMS_SCRIPT@"> - LANG=C Rscript $__tool_directory__/xcms.r + LC_ALL=C Rscript $__tool_directory__/xcms.r </token> <token name="@COMMAND_LOG_EXIT@"> @@ -117,55 +116,14 @@ </data> </xml> - <xml name="input_tic_bpc_pdf"> - <param name="tic_bpc_pdf" type="boolean" checked="False" label="Do you want TIC and BCP in PDF Format" help="Whatever, you will be able to use MultiQC tools on the tabular files" /> - </xml> - - <xml name="test_retcor_param"> - <param name="methods|method" value="peakgroups"/> - <param name="methods|smooth" value="loess"/> - <param name="methods|extra" value="1"/> - <param name="methods|missing" value="1"/> - <param name="methods|options|option" value="show"/> - <param name="methods|options|span" value="0.2"/> - <param name="methods|options|family" value="gaussian"/> - <param name="methods|options|plottype" value="deviation"/> - </xml> - - <xml name="test_retcor_output" token_raworcorrected=""> - <output name="log"> - <assert_contents> - <has_text text="object with 4 samples" /> - <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> - <has_text text="Mass range: 200.1-600 m/z" /> - <has_text text="Peaks: 9251 (about 2313 per sample)" /> - <has_text text="Peak Groups: 0" /> - <has_text text="Sample classes: KO, WT" /> - </assert_contents> - </output> - <output_collection name="ticsCorrectedTabCollection" type="list"> - <element name="ko15" value="ko15-TIC@RAWORCORRECTED@_mqc.out" /> - <element name="ko16" value="ko16-TIC@RAWORCORRECTED@_mqc.out" /> - <element name="wt15" value="wt15-TIC@RAWORCORRECTED@_mqc.out" /> - <element name="wt16" value="wt16-TIC@RAWORCORRECTED@_mqc.out" /> - </output_collection> - <output_collection name="bpcsCorrectedTabCollection" type="list"> - <element name="ko15" value="ko15-BPC@RAWORCORRECTED@_mqc.out" /> - <element name="ko16" value="ko16-BPC@RAWORCORRECTED@_mqc.out" /> - <element name="wt15" value="wt15-BPC@RAWORCORRECTED@_mqc.out" /> - <element name="wt16" value="wt16-BPC@RAWORCORRECTED@_mqc.out" /> - </output_collection> - </xml> - <token name="@HELP_AUTHORS@"> - .. 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 @@ </token> - <token name="@HELP_BCP_TIC@"> - -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. - - </token> - - <token name="@HELP_GET_PEAK_LIST@"> - -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’) - - </token> - - <token name="@HELP_GET_PEAK_LIST_OUTPUTS@"> - -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. - - </token> <xml name="citation"> <citations>
--- /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
--- 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 @@ -<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.0.0"> +<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.1.0"> <description>Merge xcms.xcmsSet xset in one to be used by group</description> <macros> @@ -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 @@ <has_text text="Sample classes: ." /> </assert_stdout> </test> + <test expect_failure="True"> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <param name="sampleMetadata" value="sampleMetadata_missing.tab" /> + <expand macro="test_file_load_single"/> + <assert_stderr> + <has_text text="Those samples are missing in your sampleMetadata: ko16" /> + </assert_stderr> + </test> </tests> <help><![CDATA[ @@ -215,6 +230,11 @@ 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