Mercurial > repos > lecorguille > xcms_xcmsset
changeset 31:e93153c07be0 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
| author | lecorguille |
|---|---|
| date | Tue, 13 Feb 2018 04:42:24 -0500 |
| parents | d71827ecd22c |
| children | 2bf1cb023c94 |
| files | README.rst abims_xcms_xcmsSet.xml destinations_input_type.py lib.r macros.xml test-data/HU_neg_017-BPC_mqc.out test-data/HU_neg_017-TIC_mqc.out test-data/MM14-BPC_mqc.out test-data/MM14-TIC_mqc.out test-data/ko15-BPC_mqc.out test-data/ko15-TIC_mqc.out test-data/ko16-BPC_mqc.out test-data/ko16-TIC_mqc.out test-data/wt15-BPC_mqc.out test-data/wt15-TIC_mqc.out test-data/wt16-BPC_mqc.out test-data/wt16-TIC_mqc.out xcms.r |
| diffstat | 18 files changed, 218 insertions(+), 14907 deletions(-) [+] |
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--- a/README.rst Thu Oct 26 11:14:49 2017 -0400 +++ b/README.rst Tue Feb 13 04:42:24 2018 -0500 @@ -22,9 +22,9 @@ Changelog/News -------------- -**Version 2.2.0 - 19/10/2017** +**Version 2.1.1 - 29/11/2017** -- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC. +- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C **Version 2.1.0 - 22/02/2017**
--- a/abims_xcms_xcmsSet.xml Thu Oct 26 11:14:49 2017 -0400 +++ b/abims_xcms_xcmsSet.xml Tue Feb 13 04:42:24 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.2.0"> +<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.1"> <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> <macros> @@ -21,6 +21,9 @@ xsetRdataOutput '$xsetRData' sampleMetadataOutput '$sampleMetadata' + ticspdf '$ticsRawPdf' + bicspdf '$bpcsRawPdf' + #if $options_scanrange.option == "show": scanrange "c($options_scanrange.scanrange)" @@ -56,13 +59,7 @@ scales "c($methods.scales)" SNR.method "$methods.SNR_method" #end if - - #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): - && mv *-TIC_mqc.out $ticsRawTab - && mv *-BPC_mqc.out $bpcsRawTab - #end if - - @COMMAND_LOG_EXIT@; + @COMMAND_LOG_EXIT@ ]]></command> <inputs> @@ -158,47 +155,39 @@ <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." /> </when> </conditional> - - - <expand macro="input_tic_bpc_pdf"/> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" /> - <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" /> - - <!-- SINGLE MODE --> - <data name="ticsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.tabular"> - <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter> - </data> - <data name="bpcsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.tabular"> - <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter> - </data> - - <!-- ZIP MODE --> <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv"> <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> </data> - <data name="ticsRawPdf" format="pdf" from_work_dir="TICs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf"> - <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> - <filter>tic_bpc_pdf</filter> - </data> - <data name="bpcsRawPdf" format="pdf" from_work_dir="BPCs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf"> - <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> - <filter>tic_bpc_pdf</filter> - </data> - <collection name="ticsRawTabCollection" type="list" label="TIC raw tabular"> - <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> - <discover_datasets pattern="(?P<designation>.+)-TIC_mqc\.out" ext="tabular" /> - </collection> - <collection name="bpcsRawTabCollection" type="list" label="BPC raw tabular"> - <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> - <discover_datasets pattern="(?P<designation>.+)-BPC_mqc\.out" ext="tabular" /> - </collection> + <data name="ticsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" /> + <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" /> + <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" /> </outputs> <tests> - <!-- + <!--<test> + <param name="input" value="sacuri_dir_root.zip" ftype="zip" /> + <param name="methods|method" value="matchedFilter" /> + <param name="methods|step" value="0.01" /> + <param name="methods|fwhm" value="4" /> + <param name="methods|options_m|option" value="show" /> + <param name="methods|options_m|max" value="50" /> + <param name="methods|options_m|snthresh" value="1" /> + <param name="methods|options_m|steps" value="2" /> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" /> + <has_text text="Mass range: 50.0021-999.9863 m/z" /> + <has_text text="Peaks: 59359 (about 14840 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> + </test> <test> <param name="input" value="sacuri_current_root.zip" ftype="zip" /> <param name="methods|method" value="centWave" /> @@ -230,21 +219,56 @@ <has_text text="Sample classes: KO, WT" /> </assert_contents> </output> - <output_collection name="ticsRawTabCollection" type="list"> - <element name="ko15" value="ko15-TIC_mqc.out" /> - <element name="ko16" value="ko16-TIC_mqc.out" /> - <element name="wt15" value="wt15-TIC_mqc.out" /> - <element name="wt16" value="wt16-TIC_mqc.out" /> - </output_collection> - <output_collection name="bpcsRawTabCollection" type="list"> - <element name="ko15" value="ko15-BPC_mqc.out" /> - <element name="ko16" value="ko16-BPC_mqc.out" /> - <element name="wt15" value="wt15-BPC_mqc.out" /> - <element name="wt16" value="wt16-BPC_mqc.out" /> - </output_collection> </test> <!-- Passed but disable to save time for Travis" --> - <!-- + <!--<test> + <param name="input" value="ko15.CDF" ftype="netcdf" /> + <param name="methods|method" value="centWave" /> + <param name="methods|ppm" value="25" /> + <param name="methods|peakwidth" value="20,50" /> + <output name="log"> + <assert_contents> + <has_text text="object with 1 samples" /> + <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" /> + <has_text text="Mass range: 200.2-600 m/z" /> + <has_text text="Peaks: 2262 (about 2262 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: ." /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="ko16.CDF" ftype="netcdf" /> + <param name="methods|method" value="centWave" /> + <param name="methods|ppm" value="25" /> + <param name="methods|peakwidth" value="20,50" /> + <output name="log"> + <assert_contents> + <has_text text="object with 1 samples" /> + <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 2408 (about 2408 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: ." /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="wt15.CDF" ftype="netcdf" /> + <param name="methods|method" value="centWave" /> + <param name="methods|ppm" value="25" /> + <param name="methods|peakwidth" value="20,50" /> + <output name="log"> + <assert_contents> + <has_text text="object with 1 samples" /> + <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" /> + <has_text text="Mass range: 200.2-599.8 m/z" /> + <has_text text="Peaks: 2278 (about 2278 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: ." /> + </assert_contents> + </output> + </test> <test> <param name="inputs|input" value="single_file" /> <param name="inputs|single_file" value="wt16.CDF" ftype="netcdf" /> @@ -277,8 +301,6 @@ <has_text text="Sample classes: ." /> </assert_contents> </output> - <output name="ticsRawTab" value="HU_neg_017-TIC_mqc.out" /> - <output name="bpcsRawTab" value="HU_neg_017-BPC_mqc.out" /> </test> <test> <param name="input" value="MM14.mzML" ftype="mzxml" /> @@ -295,8 +317,6 @@ <has_text text="Sample classes: ." /> </assert_contents> </output> - <output name="ticsRawTab" value="MM14-TIC_mqc.out" /> - <output name="bpcsRawTab" value="MM14-BPC_mqc.out" /> </test> </tests> @@ -308,6 +328,7 @@ Xcms.xcmsSet ============ +----------- Description ----------- @@ -317,16 +338,18 @@ .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf +----------------- Workflow position ----------------- **Upstream tools** -+------------------------+--------------------+-----------------------------+-----------+ -| Name | output file | format | parameter | -+------------------------+--------------------+-----------------------------+-----------+ -| Upload File | Dataset Collection | mzXML, mzML, mzData, netCDF | NA | -+------------------------+--------------------+-----------------------------+-----------+ +========================= ================= ======= ========= +Name output file format parameter +========================= ================= ======= ========= +NA NA zip NA +========================= ================= ======= ========= + **Downstream tools** @@ -335,89 +358,90 @@ +===========================+====================+=================+ |xcms.group | xset.RData | rdata.xcms.raw | +---------------------------+--------------------+-----------------+ +|PCA ellipsoid by factors | sampleMetadata.tsv | Tabular | ++---------------------------+--------------------+-----------------+ +|Anova | sampleMetadata.tsv | Tabular | ++---------------------------+--------------------+-----------------+ **Example of a metabolomic workflow** .. image:: xcms_xcmsset_workflow.png + +------ + +.. class:: infomark + +The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. + --------------------------------------------------- + + ----------- Input files ----------- -Choose your inputs ------------------- - +---------------------------+----------------------------------+ -| Parameter | Format | +| Parameter : num + label | Format | +===========================+==================================+ +| OR : Zip file | zip | ++---------------------------+----------------------------------+ | OR : Single file | mzXML, mzML, mzData, netCDF | +---------------------------+----------------------------------+ -| OR : Zip file | zip | -+---------------------------+----------------------------------+ + +**Choose your inputs** You have two methods for your inputs: -* Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group" - -* Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). - -Single file ------------ - -This method is recommended because: - -* Since files are uploaded indivudially, they are smaller. And so they should be able to be uploaded using the Get Data tools. + | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group" + | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). -* It allow you to launch your xcmsSet in parallele. - -You just have to create a Dataset Collection as explain in this video_ - -.. _video: http://download.workflow4metabolomics.org/docs/170510_galaxy_xcms_dataset_collection.m4v - - -Zip file --------- - -This method isn't recommended because zip file aren't really well integrated - -Steps for creating the zip file +Zip file: Steps for creating the zip file +----------------------------------------- **Step1: Creating your directory and hierarchize the subdirectories** - | **VERY IMPORTANT**: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug). - | Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild): - | - arabidopsis/wild/01.raw - | - arabidopsis/mutant/01.raw +VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug). + +Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild): +arabidopsis/wild/01.raw +arabidopsis/mutant/01.raw **Step2: Creating a zip file** - | Create your zip file (e.g.: arabidopsis.zip). +Create your zip file (e.g.: arabidopsis.zip). **Step 3 : Uploading it to our Galaxy server** - | If your zip file is less than 2Gb, you get use the Get Data tool to upload it. - | Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf). - | For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org). - | Advices for converting your files for the XCMS input +If your zip file is less than 2Gb, you get use the Get Data tool to upload it. + +Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf). -Raw file format ---------------- +For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org). -We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xcms centWave method. +Advices for converting your files for the XCMS input +---------------------------------------------------- + +We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method. **We recommend you the following parameters:** - | **Use Filtering**: True - | **Use Peak Picking**: True - | **Peak Peaking**: -Apply to MS Levels: All Levels (1-) : Centroid Mode - | **Use zlib**: 64 - | **Binary Encoding**: 64 - | **m/z Encoding**: 64 - | **Intensity Encoding**: 64 +Use Filtering: **True** + +Use Peak Picking: **True** + +Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode + +Use zlib: **64** + +Binary Encoding: **64** + +m/z Encoding: **64** + +Intensity Encoding: **64** ---------- @@ -451,16 +475,28 @@ Output files ------------ +xset.TICs_raw.pdf + + | "Total Ion Chromatograms" graph in pdf format. + +xset.BPCs_raw.pdf + + | "Base Peak Chromatograms" graph in pdf format with each class samples opposed. + +sampleMetadata.tsv + + | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed). + | This file is necessary in the Anova and PCA step of the workflow. + xset.RData: rdata.xcms.raw format | Rdata file that is necessary in the second step of the workflow "xcms.group". -@HELP_BCP_TIC@ +------ -sampleMetadata.tsv [if using zip] +.. class:: infomark - | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed). - | This file is necessary in the Batch correction and statictics steps of the workflow. +The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. --------------------------------------------------- @@ -471,20 +507,49 @@ Input files ----------- - | Dataset Collection -> build using this dataset_ - -.. _dataset: http://download.workflow4metabolomics.org/datasets/sacurine-neg-subset_mzXML.zip + | zip_file -> **sacuri.zip** Parameters ---------- - | **Method**: centWave - | **Max tolerated ppm m/z deviation in consecutive scans in ppm**: 25 - | **Min,Max peak width in seconds**: 10,40 - | **Advanced option**: show - | **Signal/Noise threshold**: 50 - | **Minimum difference in m/z for peaks with overlapping retention times**: 1 - | **Prefilter step for the first phase**: 3,100 + | Method -> **matchedFilter** + | step -> **0.01** + | fwhm -> **4** + | Advanced option -> **show** + | max: -> **50** + | snthresh -> **1** + | steps -> **2** + + +Output files +------------ + + | **1) xset.RData: RData file** + + | **2) Example of a sampleMetadata.tsv :** + + ++---------------------------+------------+---------+ +| sampleMetadata | class | polarity| ++===========================+============+=========+ +|HU_neg_017 | bio |negative | ++---------------------------+------------+---------+ +|HU_neg_028 | bio |negative | ++---------------------------+------------+---------+ +|HU_neg_034 | bio |negative | ++---------------------------+------------+---------+ +|Blanc04 | blank |negative | ++---------------------------+------------+---------+ +|Blanc06 | blank |negative | ++---------------------------+------------+---------+ +|Blanc09 | blank |negative | ++---------------------------+------------+---------+ + + + + | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :** + +.. image:: xcms_tics.png --------------------------------------------------- @@ -492,9 +557,9 @@ Changelog/News -------------- -**Version 2.2.0 - 19/10/2017** +**Version 2.1.1 - 29/11/2017** -- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC. +- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C **Version 2.1.0 - 22/02/2017**
--- a/destinations_input_type.py Thu Oct 26 11:14:49 2017 -0400 +++ b/destinations_input_type.py Tue Feb 13 04:42:24 2018 -0500 @@ -16,8 +16,11 @@ inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) input_extension = inp_data[ "input" ].extension - log.debug("The input extension is %s" % input_extension) - if input_extension in ["mzxml","mzml","mzdata","netcdf"]: - return 'thread1-mem_free10' - else: # zip file - return 'thread4-men_free10' + if 'input' in inp_data: + input_extension = inp_data[ "input" ].extension + log.debug("The input extension is %s" % input_extension) + if input_extension in ["mzxml","mzml","mzdata","netcdf"]: + return 'thread1-mem_free8' + # zip file + return 'thread9-mem_free8' +
--- a/lib.r Thu Oct 26 11:14:49 2017 -0400 +++ b/lib.r Tue Feb 13 04:42:24 2018 -0500 @@ -51,42 +51,6 @@ write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) } -#@author G. Le Corguille -exportTicBpcTabular <- function(dataset, filenameBase, ticORbpc, rt='raw') { - - rawORcorrected = '' - title = '' - if (rt=='corrected') { - rawORcorrected = '_corrected' - title = ' corrected by retcor' - } - - if (ticORbpc == "TIC") { - section_name = paste0('TIC',rawORcorrected) - title = paste0('Total Ion Current (TIC) chromatogram',title) - description = 'Sum of intensity (Y) of all ions detected at each retention time(X)' - } else if (ticORbpc == "BPC") { - section_name = paste0('BPC',rawORcorrected) - title = paste0('Base Peak Chromatogram (BPC)',title) - description = 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' - } - - filename=paste0(basename(file_path_sans_ext(filenameBase)),"-",ticORbpc,rawORcorrected,"_mqc.out") - - # Headers for MultiQC - cat("# file_format: 'tsv'\n", sep="", file = filename) - cat("# section_name: '",section_name,"'\n", sep="", file = filename, append = T) - cat("# title: '",title,"'\n", sep="", file = filename, append = T) - cat("# description: '",description,"'\n", sep="", file = filename, append = T) - cat("# plot_type: 'linegraph'\n", sep="", file = filename, append = T) - cat("# pconfig:\n", sep="", file = filename, append = T) - cat("# id: '",ticORbpc,rawORcorrected,"_lineplot'\n", sep="", file = filename, append = T) - cat("# ylab: 'Base Peak Intensity'\n", sep="", file = filename, append = T) - cat("# xlab: 'Retention Time'\n", sep="", file = filename, append = T) - cat("Intensity\tRT\n", file = filename, append = T) - write.table(dataset, filename ,row.names = F, col.names = F, sep = "\t", append = T, quote = F) -} - #@author Y. Guitton getBPC <- function(file,rtcor=NULL, ...) { object <- xcmsRaw(file) @@ -130,9 +94,6 @@ rtcor <- NULL TIC[[j]] <- getBPC(files[j],rtcor=rtcor) - - exportTicBpcTabular(TIC[[j]], files[j], "BPC", rt=rt) - # TIC[[j]][,1]<-rtcor } @@ -260,8 +221,6 @@ rtcor <- xcmsSet@rt$corrected[[i]] else rtcor <- NULL TIC[[i]] <- getTIC(files[i],rtcor=rtcor) - - exportTicBpcTabular(TIC[[i]], files[i], "TIC", rt=rt) } pdf(pdfname,w=16,h=10) @@ -517,7 +476,7 @@ # This function get the raw file path from the arguments -getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) { +getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) { if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]] if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]] if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]
--- a/macros.xml Thu Oct 26 11:14:49 2017 -0400 +++ b/macros.xml Tue Feb 13 04:42:24 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>
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--- a/test-data/HU_neg_017-TIC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2042 +0,0 @@ -# file_format: 'tsv' -# section_name: 'TIC' -# title: 'Total Ion Current (TIC) chromatogram' -# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'TIC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -0.7297 14106990.5361328 -0.8794 9702481.47021484 -1.3837 8129613.19750977 -1.9176 7013125.42675781 -2.4696 9278641.06665039 -2.9744 8570874.19189453 -3.4938 11163158.0219727 -3.9999 10349479.0791016 -4.5139 9556619.21386719 -5.0289 7739630.49365234 -5.5646 8598839.17749023 -6.0832 10851263.8920898 -6.5894 10000967.6911621 -7.1015 7515181.89282227 -7.6362 9577361.25683594 -8.1449 9362064.20629883 -8.6613 9248984.90795898 -9.1776 10816742.3383789 -9.6809 9584463.140625 -10.2005 10628053.0246582 -10.7068 9992136.63671875 -11.2194 7851853.5637207 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--- a/test-data/MM14-BPC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,122 +0,0 @@ -# file_format: 'tsv' -# section_name: 'BPC' -# title: 'Base Peak Chromatogram (BPC)' -# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'BPC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -270.334 1685 -270.671 1694 -271.007 4403 -271.343 11692 -271.68 26379 -272.016 41575 -272.353 56979 -272.689 72874 -273.025 80132 -273.362 76688 -273.698 76185 -274.034 68516 -274.371 55885 -274.707 46243 -275.043 33703 -275.38 24345 -275.716 16819 -276.052 12697 -276.389 9737 -276.725 6468 -277.061 8173 -277.399 8042 -277.735 10527 -278.072 11319 -278.408 9026 -278.744 11002 -279.081 17475 -279.417 22880 -279.753 25860 -280.089 28207 -280.426 30037 -280.762 27598 -281.098 24965 -281.435 23259 -281.771 17820 -282.107 13317 -282.444 9718 -282.78 7422 -283.116 4791 -283.453 3929 -283.789 2568 -284.126 2114 -284.463 1353 -284.799 2122 -285.135 1716 -285.476 2516 -285.812 3208 -286.148 3946 -286.485 5360 -286.821 6737 -287.157 8082 -287.495 10490 -287.832 10049 -288.168 10337 -288.505 9906 -288.841 8589 -289.177 6956 -289.514 6396 -289.85 4798 -290.186 3746 -290.523 2378 -290.859 2372 -291.195 1466 -291.531 828 -291.868 631 -292.204 547 -292.54 655 -292.877 625 -293.213 660 -293.549 1119 -293.886 1014 -294.222 1429 -294.558 1563 -294.895 2366 -295.231 2088 -295.567 1539 -295.903 1274 -296.24 960 -296.576 754 -296.912 507 -297.249 861 -297.586 1044 -297.923 922 -298.259 1603 -298.595 2921 -298.932 4648 -299.268 6571 -299.604 7845 -299.941 8987 -300.277 8800 -300.613 8081 -300.95 7442 -301.286 6708 -301.622 5602 -301.958 4190 -302.295 2838 -302.631 2295 -302.968 1931 -303.304 1393 -303.641 795 -303.977 1000 -304.314 1377 -304.65 1489 -304.986 1258 -305.323 1146 -305.659 1371 -305.995 1294 -306.332 1200 -306.668 1350 -307.004 1327 -307.34 1973 -307.678 2404
--- a/test-data/MM14-TIC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,122 +0,0 @@ -# file_format: 'tsv' -# section_name: 'TIC' -# title: 'Total Ion Current (TIC) chromatogram' -# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'TIC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -270.334 64989 -270.671 67476 -271.007 77870 -271.343 105126 -271.68 155634 -272.016 212782 -272.353 268032 -272.689 316565 -273.025 340331 -273.362 338131 -273.698 335301 -274.034 307674 -274.371 271946 -274.707 234750 -275.043 195146 -275.38 161970 -275.716 136385 -276.052 128592 -276.389 123558 -276.725 121014 -277.061 127507 -277.399 126646 -277.735 130228 -278.072 132416 -278.408 132485 -278.744 124922 -279.081 125163 -279.417 124318 -279.753 123363 -280.089 120277 -280.426 118986 -280.762 113485 -281.098 107102 -281.435 101458 -281.771 90191 -282.107 83128 -282.444 77062 -282.78 75613 -283.116 71773 -283.453 67160 -283.789 66865 -284.126 65476 -284.463 65096 -284.799 65391 -285.135 64007 -285.476 67614 -285.812 67987 -286.148 71023 -286.485 74579 -286.821 76881 -287.157 80532 -287.495 84444 -287.832 82377 -288.168 84165 -288.505 85163 -288.841 83033 -289.177 76825 -289.514 75184 -289.85 69372 -290.186 68449 -290.523 67203 -290.859 67735 -291.195 65109 -291.531 62919 -291.868 62332 -292.204 61394 -292.54 63670 -292.877 63974 -293.213 63777 -293.549 66847 -293.886 69879 -294.222 67201 -294.558 68828 -294.895 70897 -295.231 69083 -295.567 68382 -295.903 66991 -296.24 67648 -296.576 65762 -296.912 63895 -297.249 62145 -297.586 62027 -297.923 64304 -298.259 67216 -298.595 73178 -298.932 75116 -299.268 78789 -299.604 87023 -299.941 88688 -300.277 87898 -300.613 88769 -300.95 86435 -301.286 82923 -301.622 75966 -301.958 71102 -302.295 69901 -302.631 67821 -302.968 63912 -303.304 64266 -303.641 65557 -303.977 65430 -304.314 66124 -304.65 65862 -304.986 68685 -305.323 68801 -305.659 67658 -305.995 68467 -306.332 67208 -306.668 67104 -307.004 68460 -307.34 70357 -307.678 75178
--- a/test-data/ko15-BPC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1288 +0,0 @@ -# file_format: 'tsv' -# section_name: 'BPC' -# title: 'Base Peak Chromatogram (BPC)' -# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'BPC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -2501.378 43888 -2502.943 43960 -2504.508 43392 -2506.073 42632 -2507.638 42200 -2509.203 42288 -2510.768 42664 -2512.333 42480 -2513.898 42320 -2515.463 42528 -2517.028 43376 -2518.593 44240 -2520.158 44696 -2521.722 44560 -2523.287 44112 -2524.852 43936 -2526.417 43736 -2527.982 42912 -2529.547 42360 -2531.112 43128 -2532.677 43880 -2534.242 44104 -2535.807 44256 -2537.372 44664 -2538.937 44600 -2540.502 44224 -2542.067 44120 -2543.632 44328 -2545.197 44536 -2546.762 44872 -2548.327 44592 -2549.892 43600 -2551.457 42872 -2553.022 43528 -2554.586 44072 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285120 -2654.744 334464 -2656.308 369856 -2657.873 387136 -2659.438 393344 -2661.003 395904 -2662.568 395456 -2664.133 391936 -2665.698 396608 -2667.263 419008 -2668.828 465280 -2670.393 526336 -2671.958 586624 -2673.523 625472 -2675.088 642304 -2676.653 651392 -2678.218 664256 -2679.783 672064 -2681.348 664448 -2682.913 642048 -2684.478 611776 -2686.043 577216 -2687.608 537408 -2689.172 489984 -2690.737 437248 -2692.302 385536 -2693.867 336256 -2695.432 287104 -2696.997 240512 -2698.562 201024 -2700.127 166656 -2701.692 137088 -2703.257 117720 -2704.822 98584 -2706.387 81576 -2707.952 66760 -2709.517 53440 -2711.082 41984 -2712.647 37808 -2714.212 37464 -2715.777 37832 -2717.342 38328 -2718.907 38720 -2720.472 38992 -2722.037 39120 -2723.601 38968 -2725.166 38728 -2726.731 38912 -2728.296 38984 -2729.861 38640 -2731.426 37584 -2732.991 36608 -2734.556 36312 -2736.121 36920 -2737.686 37592 -2739.251 52864 -2740.816 76280 -2742.381 101448 -2743.946 125712 -2745.511 147648 -2747.076 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--- a/test-data/ko15-TIC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1288 +0,0 @@ -# file_format: 'tsv' -# section_name: 'TIC' -# title: 'Total Ion Current (TIC) chromatogram' -# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'TIC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -2501.378 621512 -2502.943 628280 -2504.508 631958 -2506.073 628012 -2507.638 631396 -2509.203 641593 -2510.768 647566 -2512.333 647653 -2513.898 655215 -2515.463 650586 -2517.028 652966 -2518.593 649119 -2520.158 649768 -2521.722 655132 -2523.287 648885 -2524.852 648652 -2526.417 643983 -2527.982 638764 -2529.547 640822 -2531.112 638449 -2532.677 638841 -2534.242 640496 -2535.807 635787 -2537.372 634327 -2538.937 635962 -2540.502 632008 -2542.067 634027 -2543.632 630049 -2545.197 623632 -2546.762 618731 -2548.327 623614 -2549.892 624668 -2551.457 621986 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--- a/test-data/ko16-TIC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1288 +0,0 @@ -# file_format: 'tsv' -# section_name: 'TIC' -# title: 'Total Ion Current (TIC) chromatogram' -# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'TIC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -2501.378 440346 -2502.943 443434 -2504.508 452824 -2506.073 458665 -2507.638 463178 -2509.203 470153 -2510.767 475420 -2512.332 484818 -2513.897 489902 -2515.462 495968 -2517.027 498806 -2518.592 501474 -2520.157 500080 -2521.722 498636 -2523.287 494826 -2524.852 492506 -2526.417 494692 -2527.982 500734 -2529.547 504660 -2531.112 505991 -2532.677 503059 -2534.242 504150 -2535.807 502422 -2537.372 506450 -2538.937 508703 -2540.502 510976 -2542.067 511967 -2543.632 516638 -2545.196 515202 -2546.761 516154 -2548.326 517365 -2549.891 512913 -2551.456 501514 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--- a/test-data/wt15-BPC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1288 +0,0 @@ -# file_format: 'tsv' -# section_name: 'BPC' -# title: 'Base Peak Chromatogram (BPC)' -# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'BPC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -2501.378 44464 -2502.943 44632 -2504.508 45232 -2506.073 46200 -2507.638 46592 -2509.203 46376 -2510.768 45760 -2512.333 45632 -2513.898 45152 -2515.463 44280 -2517.028 43360 -2518.592 43768 -2520.157 44536 -2521.722 45072 -2523.287 44528 -2524.852 43632 -2526.417 42944 -2527.982 42520 -2529.547 41968 -2531.112 41312 -2532.677 40832 -2534.242 40624 -2535.807 40288 -2537.372 40144 -2538.937 40240 -2540.502 40488 -2542.067 40624 -2543.632 40688 -2545.197 41640 -2546.762 43840 -2548.327 45816 -2549.892 45248 -2551.457 43200 -2553.021 41936 -2554.586 42776 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--- a/test-data/wt16-BPC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1288 +0,0 @@ -# file_format: 'tsv' -# section_name: 'BPC' -# title: 'Base Peak Chromatogram (BPC)' -# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'BPC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -2501.378 7215 -2502.943 6822 -2504.508 6494 -2506.073 6320 -2507.637 6170 -2509.202 6156 -2510.767 6396 -2512.332 6604 -2513.897 6359 -2515.462 5780 -2517.027 6312 -2518.592 7516 -2520.157 8656 -2521.722 9407 -2523.287 9831 -2524.852 9774 -2526.417 9682 -2527.982 9355 -2529.547 8781 -2531.112 7754 -2532.677 6733 -2534.242 6062 -2535.807 6317 -2537.372 6341 -2538.937 6049 -2540.502 5491 -2542.066 5558 -2543.631 5818 -2545.196 5838 -2546.761 6333 -2548.326 6442 -2549.891 6227 -2551.456 6176 -2553.021 6268 -2554.586 6404 -2556.151 6447 -2557.716 6589 -2559.281 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--- a/test-data/wt16-TIC_mqc.out Thu Oct 26 11:14:49 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1288 +0,0 @@ -# file_format: 'tsv' -# section_name: 'TIC' -# title: 'Total Ion Current (TIC) chromatogram' -# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'TIC_lineplot' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Intensity RT -2501.378 364122 -2502.943 368599 -2504.508 366635 -2506.073 370143 -2507.637 367549 -2509.202 369586 -2510.767 372421 -2512.332 378793 -2513.897 385235 -2515.462 388989 -2517.027 390943 -2518.592 392489 -2520.157 391143 -2521.722 397327 -2523.287 401857 -2524.852 400293 -2526.417 400302 -2527.982 397295 -2529.547 394008 -2531.112 387712 -2532.677 381245 -2534.242 376619 -2535.807 380812 -2537.372 381306 -2538.937 382864 -2540.502 381995 -2542.066 380836 -2543.631 381506 -2545.196 381985 -2546.761 383678 -2548.326 385813 -2549.891 387231 -2551.456 388878 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--- a/xcms.r Thu Oct 26 11:14:49 2017 -0400 +++ b/xcms.r Tue Feb 13 04:42:24 2018 -0500 @@ -13,7 +13,7 @@ # ----- PACKAGE ----- cat("\tPACKAGE INFO\n") #pkgs=c("xcms","batch") -pkgs=c("tools","parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") +pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") for(pkg in pkgs) { suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") @@ -65,6 +65,10 @@ } #saving the specific parameters +rplotspdf = "Rplots.pdf" +if (!is.null(listArguments[["rplotspdf"]])){ + rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL +} sampleMetadataOutput = "sampleMetadata.tsv" if (!is.null(listArguments[["sampleMetadataOutput"]])){ sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL @@ -90,6 +94,11 @@ intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL } +if (thefunction %in% c("xcmsSet","retcor")) { + ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL + bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL +} + if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { if (!exists("singlefile")) singlefile=NULL @@ -138,7 +147,7 @@ #change the default display settings #dev.new(file="Rplots.pdf", width=16, height=12) -pdf(file="Rplots.pdf", width=16, height=12) +pdf(file=rplotspdf, width=16, height=12) if (thefunction == "group") { par(mfrow=c(2,2)) } @@ -188,12 +197,12 @@ if (thefunction == "xcmsSet") { cat("\t\tGET TIC GRAPH\n") sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) - getTICs(xcmsSet=xset, rt="raw") - getBPCs(xcmsSet=xset, rt="raw") + getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw") + getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf) } else if (thefunction == "retcor") { cat("\t\tGET TIC GRAPH\n") - getTICs(xcmsSet=xset, rt="corrected") - getBPCs(xcmsSet=xset, rt="corrected") + getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected") + getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf) } if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {