# HG changeset patch # User ethevenot # Date 1493822948 14400 # Node ID 4753e64cf694376a287a9bb25276b82fda77a6d0 # Parent 39ccace7727003e0a37f41aa071a1b2d7f98b636 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51 diff -r 39ccace77270 -r 4753e64cf694 README.md --- a/README.md Sun Mar 26 17:37:12 2017 -0400 +++ b/README.md Wed May 03 10:49:08 2017 -0400 @@ -7,11 +7,11 @@ ### Description -**Version:** 3.0.0 -**Date:** 2017-03-21 +**Version:** 3.0.4 +**Date:** 2017-05-02 **Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) -**Citation:** Delabriere A., Hohenester U., Junot C. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. +**Citation:** Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. **Licence:** CeCILL **Reference history:** **Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) @@ -38,8 +38,8 @@ ```r source("http://www.bioconductor.org/biocLite.R") biocLite("xcms") + biocLite("plasFIA") biocLite("proFIA") - biocLite("plasFIA") ``` ### Tests @@ -53,7 +53,19 @@ ### Working example -### News +### News + +###### CHANGES IN VERSION 3.0.4 + +MINOR MODIFICATION + + * Details added in the documentation + +###### CHANGES IN VERSION 3.0.2 + +NEW FEATURE + + * Parallel processing ###### CHANGES IN VERSION 3.0.0 diff -r 39ccace77270 -r 4753e64cf694 build.xml --- a/build.xml Sun Mar 26 17:37:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 39ccace77270 -r 4753e64cf694 profia_config.xml --- a/profia_config.xml Sun Mar 26 17:37:12 2017 -0400 +++ b/profia_config.xml Wed May 03 10:49:08 2017 -0400 @@ -1,4 +1,4 @@ - + Preprocessing of FIA-HRMS data @@ -7,6 +7,8 @@ r-maxLik r-minpack.lm r-pracma + bioconductor-xcms + bioconductor-plasFIA bioconductor-proFIA @@ -14,7 +16,7 @@ - Rscript $__tool_directory__/profia_wrapper.R #if $inputs.input == "lib": @@ -33,7 +35,7 @@ variableMetadata_out "$variableMetadata_out" figure "$figure" information "$information" - ]]> + @@ -42,7 +44,7 @@ - + @@ -73,7 +75,15 @@ - + + + + + + + + + @@ -89,7 +99,7 @@ **Please cite** -Delabriere A., Hohenester U., Junot C. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. +Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. --------------------------------------------------- @@ -110,7 +120,7 @@ --------------------------------------------------- ========================================================== -*proFIA*: Preprocessing workflow for FIA-HRMS data +*proFIA*: A preprocessing workflow for FIA-HRMS data ========================================================== ----------- @@ -132,9 +142,9 @@ **References** | Delabriere A., Hohenester U., Junot C. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. -| Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29. -| Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080. -| Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303. +| Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29. (http://dx.doi.org/10.1007/s11306-012-0449-x) +| Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080. (http://dx.doi.org/10.1021/ac201267k) +| Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303. (http://dx.doi.org/10.1021/ac7024915) --------------------------------------------------- @@ -155,9 +165,15 @@ | 1 : Choose your inputs | zip | +---------------------------+------------+ +--------------------------------------------------- + +.. class:: warningmark + +VERY IMPORTANT: Your data must be in **centroid** mode (centroidization of raw files and conversion to an open format can be achieved with the proteowizard software: http://proteowizard.sourceforge.net/). + You have two methods for your inputs: - | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). + | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories; see below). | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories. **Steps for creating the zip file** @@ -167,33 +183,34 @@ .. class:: warningmark 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 +1a) Prepare a parent folder with the name of your data set (e.g., 'arabidopsis') containing your files: + | 'arabidopsis/w1.raw' + | 'arabidopsis/w2.raw' + | ... + | 'arabidopsis/m1.raw' + | 'arabidopsis/m2.raw' + | ... + | + +1b) If you have several experimental conditions resulting in distinct profiles of your samples (e.g. 'wild-type' and 'mutant' genotypes), create subfolders for your files (e.g., 'wild' and 'mutant') into your parent folder: + | 'arabidopsis/wild/w1.raw' + | 'arabidopsis/wild/w2.raw' + | ... + | 'arabidopsis/mutant/m1.raw' + | 'arabidopsis/mutant/m2.raw' + | ... + | + **Step2: Creating a zip file** -Create your zip file (e.g.: arabidopsis.zip). + | Zip your **parent** folder (here the 'arabidopsis' folder) containing all the subfolders and files with **7Zip**. + | **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** - -.. class:: warningmark - -VERY IMPORTANT: your data must be in **centroid** mode. In addition, we recommend you to convert your raw files to mzXML. - -We recommend 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** + | If your zip file is less than 2Gb, you get use the **Upload File** tool and the **no_unzip.zip** type 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). + | ---------- Parameters @@ -258,6 +275,21 @@ NEWS ---- +CHANGES IN VERSION 3.0.4 +======================== + +MINOR MODIFICATION + +Details added in the documentation + +CHANGES IN VERSION 3.0.2 +======================== + +NEW FEATURE + +Parallel processing + + CHANGES IN VERSION 3.0.0 ======================== @@ -270,7 +302,7 @@ @Article{DelabriereSubmitted, Title = {proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry}, - Author = {Delabriere, Alexis and Hohenester, Ulli and Junot, Christophe and Thevenot, Etienne A}, + Author = {Delabriere, Alexis and Hohenester, Ulli and Colsch, Benoit and Junot, Christophe and Fenaille, Francois and Thevenot, Etienne A}, Journal = {submitted}, Year = {submitted}, Pages = {--}, diff -r 39ccace77270 -r 4753e64cf694 profia_wrapper.R --- a/profia_wrapper.R Sun Mar 26 17:37:12 2017 -0400 +++ b/profia_wrapper.R Wed May 03 10:49:08 2017 -0400 @@ -97,7 +97,7 @@ fiaset <- proFIAset(directory, ppm = as.numeric(argVc["ppmN"]), - parallel = FALSE) + parallel = TRUE) stpI <- stpI + 1 @@ -182,8 +182,8 @@ row.names = FALSE, sep = "\t") -samDF <- cbind.data.frame(sampleMetadata = rownames(samDF), - samDF) +samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"], + class = samDF[, "class"]) write.table(samDF, file = argVc["sampleMetadata_out"], quote = FALSE, diff -r 39ccace77270 -r 4753e64cf694 runit/output/dataMatrix.tsv --- a/runit/output/dataMatrix.tsv Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/dataMatrix.tsv Wed May 03 10:49:08 2017 -0400 @@ -1,39 +1,42 @@ dataMatrix C100a C100b C100c M86.0965 1313797.61844021 2346283.61756864 2199831.8940868 +M89.5728 NA NA NA M89.5775 NA NA NA M89.5944 NA NA NA M89.6051 NA NA NA M90.9767 5106007.35482488 6564507.32105305 6447733.55546476 -M93.9829 NA NA NA +M93.9748 NA NA NA +M93.9834 NA NA NA +M93.9846 NA NA NA M93.9873 NA NA NA +M93.9889 NA NA NA M93.9950 NA NA NA M94.0000 NA NA NA M94.0078 NA NA NA M94.0124 NA NA NA -M94.0234 NA NA NA +M94.0174 NA NA NA +M94.0209 NA NA NA M94.0262 NA NA NA M94.0321 NA NA NA M94.0362 NA NA NA M94.0401 NA NA NA -M94.0425 NA NA NA +M94.0412 NA NA NA M94.0437 NA NA NA M94.0552 NA NA NA -M94.0991 NA NA NA M94.1052 NA NA NA M94.1167 NA NA NA -M94.1242 NA 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22506857.0327746 M581.3682 10515939.51269 7931579.45100295 7301159.9418262 M582.3124 5077956.48683686 4600378.57086312 3599079.86995104 M590.3225 101746549.313492 95557744.5944848 88043292.0021999 -M591.3258 28465733.7176523 26508076.1209476 25883926.9252266 +M591.3258 28465733.7176523 26508076.1209476 26008374.9571023 M591.4959 NA 2405858.20363335 1667892.5401486 M592.3292 3805771.55155463 3215590.36428314 3058976.81353684 M597.3453 5558354.05706274 4403047.38929835 4355193.43271536 @@ -631,18 +635,18 @@ M603.3657 8866479.3939369 8287382.94272769 7198294.20470507 M604.3689 2586954.41154763 2988375.90604904 2523725.23798267 M607.5661 1113445.3888372 1501212.91393093 1537224.91922729 -M619.5271 11747813.7439383 15463697.128246 13837978.9843392 +M619.5272 11747813.7439383 15463697.128246 14337364.5464228 M620.5304 3761561.01993107 4734963.03755274 5069530.54653342 M623.1356 3180595.5891105 4042278.55956248 4228273.45887652 M624.1388 724343.122602858 695987.647308726 NA -M629.1524 2572860.64592934 2948342.74173428 3090087.27795212 +M629.1524 2572860.64592934 3105442.1556365 3090087.27795212 M635.5011 3243038.04892189 4424993.42338596 4436907.41009134 M637.3638 2153320.20402197 1829873.68603118 NA M645.1048 849221.536255017 NA 1006127.8677095 -M645.1175 2526576.40738937 3142328.0338279 2962154.66068822 -M647.5584 15067023.1938918 16336177.8854976 18728177.9938016 +M645.1176 2526576.40738937 3142328.0338279 2962154.66068822 +M647.5585 15067023.1938918 18399786.5062587 18552943.5720032 M648.5619 6254605.04424434 8193008.61511028 7024234.43709767 -M651.1343 1987468.79138313 2507140.87094772 2375049.76869229 +M651.1344 1987468.79138313 2507140.87094772 2760554.45889613 M660.0821 814437.300289444 1534479.22412678 562744.881718695 M661.0824 2398892.29202539 2727254.79533067 4415848.32046208 M662.5694 2779079.65330773 2482375.43135903 2480001.0808934 @@ -659,9 +663,8 @@ M676.0468 1461863.10195596 NA 1377422.71456078 M683.0643 1259780.56399135 1322143.83574079 1552769.07139395 M683.5431 1732441.67345777 2525723.18668878 2647724.55411367 -M685.4360 1190057.97079061 NA 1419229.5914531 M686.4051 32080808.6893522 28761754.7656157 25571217.8418349 -M687.4083 13246103.1481081 13951215.1330508 8069238.27678928 +M687.4084 13246103.1481081 13951215.1330508 12857524.9844597 M688.4118 2093118.85466739 1814091.46550962 NA M689.0812 1476618.84097023 1741683.93653201 1913192.51839009 M689.3530 NA 1238431.80913389 1029803.46358456 @@ -686,27 +689,27 @@ M758.5692 24171669.9177599 26133048.4446723 29823488.7144675 M759.5727 11996299.5830951 12396459.816729 13725260.4161819 M760.5758 2312542.05691645 1797714.30089578 2433944.0644655 -M760.5849 8704293.57954915 9171699.09361031 11678909.7038509 -M760.5849_2 8704293.57954915 9171699.09361031 11678909.7038509 +M760.5849 8704293.57954915 10886827.6669751 11678909.7038509 +M760.5849_2 8704293.57954915 10886827.6669751 11678909.7038509 M761.5882 3494168.58240472 3623908.83475874 3517772.49370049 M780.5512 26678287.0199592 33917501.213975 35599330.0192635 -M781.5548 13370049.3355155 6786254.01813485 17495405.1874264 +M781.5550 13370049.3355155 16457198.8296785 17495405.1874264 M782.5673 8275387.67127943 13698705.3298253 14111642.4412243 -M783.5710 5090990.23826268 2775887.5304272 6341089.95006743 +M783.5714 5090990.23826268 7362752.56612007 7714528.34789568 M784.5848 5220940.29954109 4276780.46147111 6260943.09565952 M785.5880 1686702.15583167 2124120.66042257 1712214.24956577 -M786.6004 10857162.7919506 8697613.9851878 12499433.8991773 +M786.6004 10857162.7919506 12918268.1405544 12499433.8991773 M787.6038 4761674.55928992 5879054.35089474 7047984.21331802 M795.5018 2077762.78637069 NA 1907175.50675846 M796.5253 4271079.60468799 3501147.38860042 5343302.22793834 M796.5462 NA 2822281.02903116 3224036.730931 M804.5512 6633582.89013492 8165455.97185418 7470168.70212077 M805.5546 2438210.55855297 3663463.1635972 3764389.21632828 -M806.5674 4467025.00798707 6619742.31219476 9583742.64770817 -M807.5718 1352704.42256487 2936768.26498869 1887270.8950478 -M808.5826 10891390.3423662 15794458.1878269 16077663.9695797 +M806.5677 NA 6619742.31219476 9583742.64770817 +M807.5712 1352704.42256487 2936768.26498869 4447312.92370322 +M808.5826 13656852.4024354 15794458.1878269 16077663.9695797 M809.5859 5995718.59407245 5735791.69055253 7082868.29906178 -M810.6004 1864314.89593087 2348128.92155743 3928135.89388521 +M810.6003 3629141.36584462 2348128.92155743 3928135.89388521 M813.6843 NA 773185.606064327 1241785.9308559 M828.5517 6912623.84509757 6836612.02012318 8339689.31073757 M829.5550 NA 2944009.16774303 4078158.50009707 diff -r 39ccace77270 -r 4753e64cf694 runit/output/figure.pdf Binary file runit/output/figure.pdf has changed diff -r 39ccace77270 -r 4753e64cf694 runit/output/information.txt --- a/runit/output/information.txt Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/information.txt Wed May 03 10:49:08 2017 -0400 @@ -1,12 +1,12 @@ -Start of the 'proFIA' Galaxy module call: Sat 25 Mar 2017 08:55:32 PM +Start of the 'proFIA' Galaxy module call: Wed 03 May 2017 01:18:28 PM files_root_directory plasFIA 1) Peak detection step ('proFIAset'): 2) Peak alignment ('group.FIA'): - 719 groups have been done . + 722 groups have been done . 3) Creating the peak table ('makeDataMatrix'): @@ -14,9 +14,9 @@ 5) Plotting ('plot'): PCA -3 samples x 648 variables +3 samples x 644 variables standard scaling of predictors -71 excluded variables (near zero variance) +78 excluded variables (near zero variance) R2X(cum) pre ort Total 1 2 0 null device @@ -25,11 +25,11 @@ 6) Printing ('show'): A "proFIAset" object containing 1 classes. Missing values have been imputed. -2161 peaks detected. -719 features have been grouped. +2101 peaks detected. +722 features have been grouped. The data matrix is avalaible. -Memory usage: 0.425 MB +Memory usage: 0.419 MB 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'): -End of 'proFIA' Galaxy module call: 2017-03-25 21:22:13 +End of 'proFIA' Galaxy module call: 2017-05-03 13:27:09 diff -r 39ccace77270 -r 4753e64cf694 runit/output/sampleMetadata.tsv --- a/runit/output/sampleMetadata.tsv Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/sampleMetadata.tsv Wed May 03 10:49:08 2017 -0400 @@ -1,4 +1,4 @@ -sampleMetadata sampleID class -1 C100a plasFIA -2 C100b plasFIA -3 C100c plasFIA +sampleMetadata samDF[, colnames(samDF) != "sampleID"] +C100a plasFIA +C100b plasFIA +C100c plasFIA diff -r 39ccace77270 -r 4753e64cf694 runit/output/variableMetadata.tsv --- a/runit/output/variableMetadata.tsv Sun Mar 26 17:37:12 2017 -0400 +++ b/runit/output/variableMetadata.tsv Wed May 03 10:49:08 2017 -0400 @@ -1,720 +1,723 @@ variableMetadata mzMed mzMin mzMax sizeSamp scanMin scanMax nPeaks meanSolvent timeShifted signalOverSolventPvalueMean corSampPeakMean corSampPeakSd signalOverSolventRatioMean imputationOk variableID -M86.0965 86.0965189329336 86.0962219238281 86.0969924926758 54 18 88 3 0 0 0 0.383749268026674 0.150206018113732 Inf 1 M86.0965 -M89.5775 89.577503377741 89.5766754150391 89.5781402587891 57 18 75 1 0 0 0 0.170385033866943 NA Inf 0 M89.5775 -M89.5944 89.5943771938108 89.5933990478516 89.5950241088867 70 18 88 1 0 0 0 0.347469211489384 NA Inf 0 M89.5944 -M89.6051 89.6051298777262 89.6045913696289 89.6056442260742 58 18 76 1 0 0 0 0.172025405242609 NA Inf 0 M89.6051 -M90.9767 90.9767083832762 90.9757690429688 90.9774398803711 55 18 92 7 27656.2421201676 0 0 0.80371588811194 0.0704725256671676 11.478958927506 1 M90.9767 -M93.9829 93.982937387518 93.9816589355469 93.9840393066406 59.5 18 79 2 3162.97825113932 0 0 0.398737330824048 0.0542641115731589 15.8271238248609 0 M93.9829 -M93.9873 93.9873293603373 93.9867324829102 93.98779296875 60 18 78 1 2481.60717773438 0 0 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934.649597167969 59 18 83 3 0 0 0 0.551469517618018 0.0583750572482909 Inf 1 M934.6468 +M935.6502 935.65021387736 935.647216796875 935.65283203125 66 18 89 3 0 0 0 0.417741101527393 0.0863762747996147 Inf 1 M935.6502 +M952.6658 952.665781030899 952.663818359375 952.668762207031 57 18 77 2 0 0 0 0.367679817255971 0.225357012575034 Inf 0 M952.6658 diff -r 39ccace77270 -r 4753e64cf694 test/test-profia --- a/test/test-profia Sun Mar 26 17:37:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -#!/bin/bash - -# Constants {{{1 -################################################################ - -PROG_PATH=$(dirname $0) - -# MAIN {{{1 -################################################################ - -$PROG_PATH/../profia_wrapper.R zipfile $PROG_PATH/../test-data/input-plasFIA.zip ppmN 2 ppmGroupN 1 fracGroupN 0.1 kI 2 dataMatrix_out $PROG_PATH/output-dataMatrix.tsv - -if ! diff "$PROG_PATH/output-dataMatrix.tsv" "$PROG_PATH/../test-data/output-dataMatrix.tsv" ; then - echo "Incorrect output data matrix." >&2 - exit 1 -fi