Mercurial > repos > ethevenot > profia
changeset 1:4753e64cf694 draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
| author | ethevenot |
|---|---|
| date | Wed, 03 May 2017 10:49:08 -0400 |
| parents | 39ccace77270 |
| children | 3f8ae071bdda |
| files | README.md build.xml profia_config.xml profia_wrapper.R runit/output/dataMatrix.tsv runit/output/figure.pdf runit/output/information.txt runit/output/sampleMetadata.tsv runit/output/variableMetadata.tsv test/test-profia |
| diffstat | 10 files changed, 853 insertions(+), 906 deletions(-) [+] |
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--- 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
--- 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 @@ -<project name="w4m.profia" default="all"> - - <property name="tool.xml" value="profia_config.xml"/> - <property name="conda.dir" value="${user.home}/w4m-conda"/> - - <!--~~~ - ~ ALL ~ - ~~~~~--> - - <target name="all"/> - - <!--~~~~ - ~ TEST ~ - ~~~~~--> - - <target name="test" depends="plain.test,planemo.lint,planemo.test"/> - - <!--~~~~~~~~~~ - ~ PLAIN TEST ~ - ~~~~~~~~~~~--> - - <target name="plain.test"> - <exec executable="test/test-profia" failonerror="true"/> - </target> - - <!--~~~~~~~~~~~~ - ~ PLANEMO LINT ~ - ~~~~~~~~~~~~~--> - - <target name="planemo.lint"> - <exec executable="planemo" failonerror="true"> - <arg value="lint"/> - <arg value="${tool.xml}"/> - </exec> - </target> - - <!--~~~~~~~~~~~~ - ~ PLANEMO TEST ~ - ~~~~~~~~~~~~~--> - - <target name="planemo.test" depends="planemo.conda.install"> - <exec executable="planemo" failonerror="true"> - <arg value="test"/> - <arg value="--conda_prefix"/> - <arg value="${conda.dir}"/> - <arg value="--galaxy_branch"/> - <arg value="release_16.07"/> - <arg value="--conda_dependency_resolution"/> - <arg value="${tool.xml}"/> - </exec> - </target> - - <!--~~~~~~~~~~~~~~~~~~~~~ - ~ PLANEMO CONDA INSTALL ~ - ~~~~~~~~~~~~~~~~~~~~~~--> - - <target name="planemo.conda.install" depends="planemo.conda.init"> - <exec executable="planemo" failonerror="true"> - <arg value="conda_install"/> - <arg value="--conda_prefix"/> - <arg value="${conda.dir}"/> - <arg value="${tool.xml}"/> - </exec> - </target> - - <!--~~~~~~~~~~~~~~~~~~ - ~ PLANEMO CONDA INIT ~ - ~~~~~~~~~~~~~~~~~~~--> - - <available file="${conda.dir}" property="conda.is.installed"/> - <target name="planemo.conda.init" unless="conda.is.installed"> - <exec executable="planemo" failonerror="true"> - <arg value="conda_init"/> - <arg value="--conda_prefix"/> - <arg value="${conda.dir}"/> - </exec> - </target> - - <!--~~~~~ - ~ CLEAN ~ - ~~~~~~--> - - <target name="clean"> - <delete dir="${conda.dir}"/> - </target> - -</project>
--- 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 @@ -<tool id="profia" name="proFIA" version="3.0.0"> +<tool id="profia" name="proFIA" version="3.0.4"> <description>Preprocessing of FIA-HRMS data</description> <requirements> @@ -7,6 +7,8 @@ <requirement type="package">r-maxLik</requirement> <requirement type="package">r-minpack.lm</requirement> <requirement type="package">r-pracma</requirement> + <requirement type="package">bioconductor-xcms</requirement> + <requirement type="package">bioconductor-plasFIA</requirement> <requirement type="package">bioconductor-proFIA</requirement> </requirements> @@ -14,7 +16,7 @@ <exit_code range="1:" level="fatal" /> </stdio> - <command><![CDATA[ + <command> Rscript $__tool_directory__/profia_wrapper.R #if $inputs.input == "lib": @@ -33,7 +35,7 @@ variableMetadata_out "$variableMetadata_out" figure "$figure" information "$information" - ]]></command> + </command> <inputs> <conditional name="inputs"> @@ -42,7 +44,7 @@ <option value="lib" >Library directory name</option> </param> <when value="zip_file"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> + <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file (see the details for file upload in the help section below)" /> </when> <when value="lib"> <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > @@ -73,7 +75,15 @@ <param name="ppmGroupN" value="1"/> <param name="fracGroupN" value="0.1"/> <param name="kI" value="2"/> - <output name="dataMatrix_out" file="output-dataMatrix.tsv"/> + <output name="dataMatrix_out" file="output-dataMatrix.tsv" /> + <output name="information"> + <assert_contents> + <has_text text="722 groups have been done" /> + <has_text text="3 samples x 644 variables" /> + <has_text text="78 excluded variables (near zero variance)" /> + <has_text text="2101 peaks detected" /> + </assert_contents> + </output> </test> </tests> @@ -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 @@ <citations> <citation type="bibtex">@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 = {--},
--- 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,
--- 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 NA NA -M94.1339 NA NA NA -M94.1356 NA NA NA -M94.1397 NA NA NA +M94.1227 NA NA NA +M94.1401 NA NA NA M94.1445 NA NA NA M94.1538 NA NA NA +M94.1559 NA NA NA M95.0604 685629.13713184 993375.02882652 875626.486232038 -M96.9218 11555241.0234047 11798830.9597099 13629842.0824619 +M96.9218 11555241.0234047 11798830.9597099 13712178.7307854 M97.0761 1114447.34533038 1167650.73440278 987109.64945019 M98.9189 3036892.14294779 2897574.20676409 2879965.62034251 M102.0550 425296.351333251 562287.354221277 NA M102.0914 3405898.45991167 3405365.30747783 NA -M103.9379 NA NA NA +M103.9195 NA NA NA M103.9419 NA NA NA M104.1070 NA NA NA M105.0699 4302867.69309973 4844241.85637734 3733356.71721098 @@ -51,45 +54,52 @@ M120.0808 2872417.82916936 2263221.21507969 2327238.94823518 M120.9661 603722.847061515 NA 573795.21966387 M121.0509 122658259.614793 104503127.137474 94239375.1646403 +M121.8984 NA NA NA M121.9045 NA NA NA -M121.9232 NA NA NA +M121.9157 NA NA NA +M121.9208 NA NA NA M121.9247 NA NA NA M121.9269 NA NA NA +M121.9312 NA NA NA M121.9333 NA NA NA M121.9391 NA NA NA -M121.9520 NA NA NA +M121.9524 NA NA NA +M121.9552 NA NA NA +M121.9704 NA NA NA M121.9738 NA NA NA -M121.9760 NA NA NA +M121.9836 NA NA NA +M121.9888 NA NA NA M121.9938 NA NA NA -M122.0100 NA NA NA +M121.9957 NA NA NA +M122.0018 NA NA NA +M122.0480 NA NA NA M122.0542 4513962.08223987 3201210.5171773 4014449.66768367 M122.0579 NA NA NA +M122.0747 NA NA NA M122.0995 NA NA NA -M122.1256 NA NA NA -M122.1598 NA NA NA -M126.1026 81499099.8245328 124635981.19873 111163001.300936 +M126.1026 81499099.8245328 124635981.19873 80083019.3531485 M127.1059 6012736.00869722 5472794.82842695 4871879.07593195 M128.0494 23952127.8478598 19058160.3422955 17601743.7731112 M129.0658 988215.070873834 1040340.62937073 854623.945932545 M130.0498 1955847.68063145 2232763.20934855 2467285.5945456 M130.0862 1085605.25319448 1465336.20457251 1829782.12060952 -M130.1087 319305323.249651 290908568.308084 265409459.287951 +M130.1087 319305323.249651 291519987.402727 265409459.287951 M131.0815 596446.53961781 691807.982855779 NA M131.1057 3682474.54143962 2036935.67466124 2660637.56292433 M131.1120 9785332.21473518 8692010.96517718 8288068.26203035 M132.0655 3790320.10909363 4035488.20961741 4165651.60338819 M132.0767 2762213.88476255 3202180.90847702 2909373.90206213 -M132.1019 58938805.9629904 60083542.3860023 57646862.9011984 +M132.1019 58938805.9629904 60083542.3860023 57978919.76802 M133.0971 1526239.14803199 1680743.18492953 1793790.93561658 M133.1052 1806771.72880841 1958263.70045634 2116383.2046456 M134.0448 563310.367045782 550778.627756037 NA -M134.0964 69015365.274054 65428953.2448955 57158814.3360672 +M134.0964 69455994.6946368 65595158.2631852 57158814.3360672 M134.9884 1350501.82892699 1316365.41719993 NA M135.0028 16443026.4661012 19052105.7436914 19213830.3866995 M135.0301 NA NA NA M135.0998 3994966.42947665 3704548.05397512 3390018.27395486 -M136.0757 39193123.0686269 35076700.2394653 34902125.3884823 -M137.0573 174483.88016119 NA 392859.082029682 +M136.0757 39193123.0686269 35201909.1549833 34902125.3884823 +M137.0573 NA NA NA M137.0790 NA NA NA M138.9065 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--- 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
--- 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
--- 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 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--- 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