| Next changeset 1:d9e05021553c (2016-08-06) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f |
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LICENSE.md README.md build.xml static/images/transformation_workflowPositionImage.png test-data/input-dataMatrix.tsv test-data/output-dataMatrix.tsv test-data/output-information.txt tests/input/dataMatrix.tsv tests/transformation_tests.R transformation_config.xml transformation_script.R transformation_wrapper.R |
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| diff -r 000000000000 -r eacea1349a7c LICENSE.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE.md Fri Jul 29 12:11:01 2016 -0400 |
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| b'@@ -0,0 +1,517 @@\n+ CeCILL FREE SOFTWARE LICENSE AGREEMENT\n+\n+Version 2.1 dated 2013-06-21\n+\n+\n+ Notice\n+\n+This Agreement is a Free Software license agreement that is the result\n+of discussions between its authors in order to ensure compliance with\n+the two main principles guiding its drafting:\n+\n+ * firstly, compliance with the principles governing the distribution\n+ of Free Software: access to source code, broad rights granted to users,\n+ * secondly, the election of a governing law, French law, with which it\n+ is conformant, both as regards the law of torts and intellectual\n+ property law, and the protection that it offers to both authors and\n+ holders of the economic rights over software.\n+\n+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) \n+license are: \n+\n+Commissariat \xe0 l\'\xe9nergie atomique et aux \xe9nergies alternatives - CEA, a\n+public scientific, technical and industrial research establishment,\n+having its principal place of business at 25 rue Leblanc, immeuble Le\n+Ponant D, 75015 Paris, France.\n+\n+Centre National de la Recherche Scientifique - CNRS, a public scientific\n+and technological establishment, having its principal place of business\n+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.\n+\n+Institut National de Recherche en Informatique et en Automatique -\n+Inria, a public scientific and technological establishment, having its\n+principal place of business at Domaine de Voluceau, Rocquencourt, BP\n+105, 78153 Le Chesnay cedex, France.\n+\n+\n+ Preamble\n+\n+The purpose of this Free Software license agreement is to grant users\n+the right to modify and redistribute the software governed by this\n+license within the framework of an open source distribution model.\n+\n+The exercising of this right is conditional upon certain obligations for\n+users so as to preserve this status for all subsequent redistributions.\n+\n+In consideration of access to the source code and the rights to copy,\n+modify and redistribute granted by the license, users are provided only\n+with a limited warranty and the software\'s author, the holder of the\n+economic rights, and the successive licensors only have limited liability.\n+\n+In this respect, the risks associated with loading, using, modifying\n+and/or developing or reproducing the software by the user are brought to\n+the user\'s attention, given its Free Software status, which may make it\n+complicated to use, with the result that its use is reserved for\n+developers and experienced professionals having in-depth computer\n+knowledge. Users are therefore encouraged to load and test the\n+suitability of the software as regards their requirements in conditions\n+enabling the security of their systems and/or data to be ensured and,\n+more generally, to use and operate it in the same conditions of\n+security. This Agreement may be freely reproduced and published,\n+provided it is not altered, and that no provisions are either added or\n+removed herefrom.\n+\n+This Agreement may apply to any or all software for which the holder of\n+the economic rights decides to submit the use thereof to its provisions.\n+\n+Frequently asked questions can be found on the official website of the\n+CeCILL licenses family (http://www.cecill.info/index.en.html) for any \n+necessary clarification.\n+\n+\n+ Article 1 - DEFINITIONS\n+\n+For the purpose of this Agreement, when the following expressions\n+commence with a capital letter, they shall have the following meaning:\n+\n+Agreement: means this license agreement, and its possible subsequent\n+versions and annexes.\n+\n+Software: means the software in its Object Code and/or Source Code form\n+and, where applicable, its documentation, "as is" when the Licensee\n+accepts the Agreement.\n+\n+Initial Software: means the Software in its Source Code and possibly its\n+Object Code form and, where applicable, its documentation, "as is" when\n+it is first distributed under the terms and conditions of the Agreement.\n+\n+Modified Software: means the Software modified by at lea'..b"l be\n+decided on a case-by-case basis between the relevant Licensor and the\n+Licensee pursuant to a memorandum of understanding. 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However, any\n+licenses that it may have granted prior to termination of the Agreement\n+shall remain valid subject to their having been granted in compliance\n+with the terms and conditions hereof.\n+\n+\n+ Article 11 - MISCELLANEOUS\n+\n+\n+ 11.1 EXCUSABLE EVENTS\n+\n+Neither Party shall be liable for any or all delay, or failure to\n+perform the Agreement, that may be attributable to an event of force\n+majeure, an act of God or an outside cause, such as defective\n+functioning or interruptions of the electricity or telecommunications\n+networks, network paralysis following a virus attack, intervention by\n+government authorities, natural disasters, water damage, earthquakes,\n+fire, explosions, strikes and labor unrest, war, etc.\n+\n+11.2 Any failure by either Party, on one or more occasions, to invoke\n+one or more of the provisions hereof, shall under no circumstances be\n+interpreted as being a waiver by the interested Party of its right to\n+invoke said provision(s) subsequently.\n+\n+11.3 The Agreement cancels and replaces any or all previous agreements,\n+whether written or oral, between the Parties and having the same\n+purpose, and constitutes the entirety of the agreement between said\n+Parties concerning said purpose. No supplement or modification to the\n+terms and conditions hereof shall be effective as between the Parties\n+unless it is made in writing and signed by their duly authorized\n+representatives.\n+\n+11.4 In the event that one or more of the provisions hereof were to\n+conflict with a current or future applicable act or legislative text,\n+said act or legislative text shall prevail, and the Parties shall make\n+the necessary amendments so as to comply with said act or legislative\n+text. All other provisions shall remain effective. Similarly, invalidity\n+of a provision of the Agreement, for any reason whatsoever, shall not\n+cause the Agreement as a whole to be invalid.\n+\n+\n+ 11.5 LANGUAGE\n+\n+The Agreement is drafted in both French and English and both versions\n+are deemed authentic.\n+\n+\n+ Article 12 - NEW VERSIONS OF THE AGREEMENT\n+\n+12.1 Any person is authorized to duplicate and distribute copies of this\n+Agreement.\n+\n+12.2 So as to ensure coherence, the wording of this Agreement is\n+protected and may only be modified by the authors of the License, who\n+reserve the right to periodically publish updates or new versions of the\n+Agreement, each with a separate number. These subsequent versions may\n+address new issues encountered by Free Software.\n+\n+12.3 Any Software distributed under a given version of the Agreement may\n+only be subsequently distributed under the same version of the Agreement\n+or a subsequent version, subject to the provisions of Article 5.3.4\n+<#compatibility>.\n+\n+\n+ Article 13 - GOVERNING LAW AND JURISDICTION\n+\n+13.1 The Agreement is governed by French law. The Parties agree to\n+endeavor to seek an amicable solution to any disagreements or disputes\n+that may arise during the performance of the Agreement.\n+\n+13.2 Failing an amicable solution within two (2) months as from their\n+occurrence, and unless emergency proceedings are necessary, the\n+disagreements or disputes shall be referred to the Paris Courts having\n+jurisdiction, by the more diligent Party.\n" |
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| diff -r 000000000000 -r eacea1349a7c README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,38 @@ +## Transformation of the data matrix +#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project + +Status: [](https://travis-ci.org/workflow4metabolomics/transformation). + +### Description + +**Version:** 2.0.2 +**Date:** 2016-07-27 +**Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) +**Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) +**Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) +**Licence:** CeCILL +**Reference history:** [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) +**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) + +### Installation + +* Configuration file: **transformation_config.xml** +* Image files: **static/images/transformation_workflowPositionImage.png** +* Wrapper file: **transformation_wrapper.R** +* R packages + + **batch** from CRAN +> install.packages("batch", dep=TRUE) + +### Tests + +The code in the wrapper can be tested by running the **tests/transformation_tests.R** in R + +### News + +##### CHANGES IN VERSION 2.0.2 + +INTERNAL MODIFICATION + + o Creating tests for R code + +*** \ No newline at end of file |
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| diff -r 000000000000 -r eacea1349a7c build.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build.xml Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,78 @@ +<project name="transformation" default="all"> + + <property name="tool.xml" value="transformation_config.xml"/> + <property name="conda.dir" value="${user.home}/w4m-conda"/> + + <!--~~~ + ~ ALL ~ + ~~~~~--> + + <target name="all"/> + + <!--~~~~ + ~ TEST ~ + ~~~~~--> + + <target name="test" depends="planemo.lint,planemo.test"/> + + <!--~~~~~~~~~~~~ + ~ PLANEMO LINT ~ + ~~~~~~~~~~~~~--> + + <target name="planemo.lint"> + <exec executable="planemo" failonerror="true"> + <arg value="lint"/> + <arg value="${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="${conda.dir}"/> + <arg value="--galaxy_branch"/> + <arg value="release_16.01"/> + <arg value="--conda_dependency_resolution"/> + <arg value="${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 ~ + ~~~~~~~~~~~~~~~~~~~--> + + <target name="planemo.conda.init"> + <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> |
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| diff -r 000000000000 -r eacea1349a7c test-data/input-dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input-dataMatrix.tsv Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,4 @@ +dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209 +HMDB01032 2569204.92420381 0 NA 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 NA 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586 +HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 0 8932005.5351622 8340827.52597275 NA 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067 +HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 NA 474901.604069803 0 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275 |
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| diff -r 000000000000 -r eacea1349a7c test-data/output-dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output-dataMatrix.tsv Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,4 @@ +dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209 +HMDB01032 6.4097989147612 0 NA 6.09997027329661 7.11526240665874 6.28089527381727 3.54358308420777 6.36050308252273 5.10891757614317 4.91314350299257 6.90867577518696 8.17485868642442 6.18865781865127 6.85146813808323 7.15041247454837 NA 5.42004776716409 6.22306306626184 4.94662022439559 7.37295492036015 7.27063523034019 6.19163514187816 4.53343349490544 5.32092215431089 7.5209776054089 5.30629545257268 7.13293402248823 5.54921399176614 6.9600320989046 7.63768158129972 +HMDB03072 6.55971722925779 4.81708905980554 5.04988105213681 6.51345803995019 4.62561366426132 5.53561712670229 6.29186119203103 7.0785753825162 6.77320937252341 6.74126089438601 6.96163569535831 6.42030803011131 6.97774244620064 6.81635039149045 6.85759304374228 6.10496929552348 0 6.95094903215397 6.92120919289027 NA 7.04990924792185 6.77226769637614 7.0715166807041 6.98082020473051 4.86757696793835 6.99964322349096 6.62408596371694 5.79516485801501 7.03759469528156 6.33681881618545 +HMDB00792 5.63303354894831 6.58968498126768 6.12407791036679 6.1359107347108 5.9264445491276 6.46954099084838 6.20794628655586 6.57287278591817 6.51749315793243 6.36374164630256 6.64387103511643 6.48334335718895 5.91684199080981 6.40195906287088 NA 5.67660455098873 0 6.47070320154497 6.28278459579123 6.24747333823543 6.7727766268923 6.21459662567008 5.54009381995067 6.02316074306626 6.37844501215531 6.262770729849 6.01144244912512 6.85002059061201 6.64031663354361 6.54356991744521 |
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| diff -r 000000000000 -r eacea1349a7c test-data/output-information.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output-information.txt Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,10 @@ + +Start of the 'Transformation' module: Thu 28 Jul 2016 03:30:03 AM + +'log10' transformation + +Missing values in the 'dataMatrix': 4 (4%) + +Zero values in the 'dataMatrix': 3 (3%) + +End of the 'Transformation' Galaxy module call: Thu 28 Jul 2016 03:30:03 AM |
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| diff -r 000000000000 -r eacea1349a7c tests/input/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/input/dataMatrix.tsv Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,4 @@ +dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209 +HMDB01032 2569204.92420381 0 NA 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 NA 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586 +HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 0 8932005.5351622 8340827.52597275 NA 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067 +HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 NA 474901.604069803 0 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275 |
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| diff -r 000000000000 -r eacea1349a7c tests/transformation_tests.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/transformation_tests.R Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,142 @@ +library(RUnit) + +wrapperF <- function(argVc) { + + source("../transformation_script.R") + + +#### Start_of_testing_code <- function() {} + + +##------------------------------ +## Initializing +##------------------------------ + +## options +##-------- + +strAsFacL <- options()[["stringsAsFactors"]] +options(stringsAsFactors=FALSE) + +## constants +##---------- + +modNamC <- "Transformation" ## module name +metVc <- c("log2", "log10") ## available methods + +topEnvC <- environment() +flagC <- "\n" + +## functions +##---------- + +flgF <- function(tesC, + envC = topEnvC, + txtC = NA) { ## management of warning and error messages + + tesL <- eval(parse(text = tesC), envir = envC) + + if(!tesL) { + + sink(NULL) + stpTxtC <- ifelse(is.na(txtC), + paste0(tesC, " is FALSE"), + txtC) + + stop(stpTxtC, + call. = FALSE) + + } + +} ## flgF + +## log file +##--------- + +sink(argVc[["information"]]) + +cat("\nStart of the '", modNamC, "' module: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + +## loading +##-------- + +datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]], + check.names = FALSE, + header = TRUE, + row.names = 1, + sep = "\t"))) + +metC <- argVc[["method"]] + +## checking +##--------- + +flgF("metC %in% metVc", txtC = paste0("Transformation method must be either '", paste(metVc, collapse = "', '"), "'")) + + +##------------------------------ +## Computation +##------------------------------ + + +datMN <- transformF(datMN = datMN, ## dataMatrix + metC = metC) ## transformation method + + +##------------------------------ +## Ending +##------------------------------ + + +## saving +##------- + +datDF <- cbind.data.frame(dataMatrix = colnames(datMN), + as.data.frame(t(datMN))) +write.table(datDF, + file = argVc[["dataMatrix_out"]], + quote = FALSE, + row.names = FALSE, + sep = "\t") + +## ending +##------- + +cat("\nEnd of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "") + +sink() + +options(stringsAsFactors = strAsFacL) + + +#### End_of_testing_code <- function() {} + + + return(list(datDF = datDF)) + + rm(list = ls()) + +} + +exaDirOutC <- "output" +file.exists(exaDirOutC) || dir.create(exaDirOutC) + +tesArgLs <- list(input_log10 = c(method = "log10", + .chkC = "checkEqualsNumeric(outLs[['datDF']]['HMDB03072', 'HU_021'], 4.817089, tolerance = 1e-6)")) + +for(tesC in names(tesArgLs)) + tesArgLs[[tesC]] <- c(tesArgLs[[tesC]], + dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"), + dataMatrix_out = file.path(exaDirOutC, "dataMatrix.tsv"), + information = file.path(exaDirOutC, "information.txt")) + +for(tesC in names(tesArgLs)) { + print(tesC) + outLs <- wrapperF(tesArgLs[[tesC]]) + if(".chkC" %in% names(tesArgLs[[tesC]])) + stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]]))) +} + +message("Checks successfully completed") |
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| diff -r 000000000000 -r eacea1349a7c transformation_config.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transformation_config.xml Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,176 @@ +<tool id="Transformation" name="Transformation" version="2.0.2; 2016-07-27"> + <description>Transforms the dataMatrix intensity values</description> + + <requirements> + <requirement type="package" version="3.2.2">R</requirement> + <requirement type="package">r-batch</requirement> + </requirements> + + <command><![CDATA[ + Rscript $__tool_directory__/transformation_wrapper.R + dataMatrix_in "$dataMatrix_in" + method "$method" + + dataMatrix_out "$dataMatrix_out" + information "$information" + ]]></command> + + <inputs> + <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" /> + <param name="method" label="Method" type="select" help=""> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> + </inputs> + + <outputs> + <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data> + <data name="information" label="${tool.name}_information.txt" format="txt"/> + </outputs> + + <tests> + <test> + <param name="dataMatrix_in" value="input-dataMatrix.tsv"/> + <param name="method" value="log10"/> + <output name="dataMatrix_out" file="output-dataMatrix.tsv"/> + </test> + </tests> + + <help> + +.. class:: infomark + +**Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA) + +--------------------------------------------------- + +.. class:: infomark + +**Tool updates** + +See the **NEWS** section at the bottom of this page + +--------------------------------------------------- + +======================== +Transformation +======================== + +----------- +Description +----------- + + | Performs transformation of the dataMatrix intensity values aimed at stabilizing variance. + | For mass spectrometry data, where multiplicative noise has been reported, logarithm transformation can be useful to make the peak intensity variance independent of the intensity mean (see for example Veselkov et al, 2011). + | For the logarithm transformations, log(1+X) is used (to avoid returning -Inf for 0 values); NA values remain unchanged + +| `Veselkov et al (2011). Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery. Analytical Chemistry, 83:5864-5872. <http://dx.doi.org/10.1021/ac201065j>`_ + +----------------- +Workflow position +----------------- + +| In the workflow example below, the intensities are first transformed, before the signal drift and batch-effects are corrected; finally, the data quality is evaluated numerically and visually. +| + +.. image:: transformation_workflowPositionImage.png + :width: 600 + + + +----------- +Input files +----------- + ++----------------------------+---------+ +| Parameter : num + label | Format | ++============================+=========+ +| 1 : Data matrix file | tabular | ++----------------------------+---------+ + +| +| **Required format for the dataMatrix is described in the HowTo entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org** +| + +---------- +Parameters +---------- + +Method + | Method to be used for transforming the intensity values of the dataMatrix: + | **log2** (resp. **log10**): intensities values are log2 (resp. log10) transformed: log(1+X) is used to avoid generating -Inf for 0 values + | in case of negative intensities in the initial dataMatrix, an error is returned + | in case of missing (NA) intensities in the initial dataMatrix, these intensities remain set to NA after transformation + +------------ +Output files +------------ + +dataMatrix_out.tabular + | dataMatrix data file with the transformed intensity values + | + +information.txt + | Text file giving some informations about the computation (eg, number of NA and 0 values in the initial dataMatrix) + | + +--------------------------------------------------- + +--------------- +Working example +--------------- + +.. class:: infomark + +See the **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu + +--------------------------------------------------- + +---- +NEWS +---- + +CHANGES IN VERSION 2.0.2 +======================== + +INTERNAL MODIFICATIONS + +Creating tests for R code + + </help> + + <citations> + <citation type="bibtex">@Article{Thevenot2015, + Title = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses}, + Author = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe}, + Journal = {Journal of Proteome Research}, + Year = {2015}, + Note = {PMID: 26088811}, + Number = {8}, + Pages = {3322-3335}, + Volume = {14}, + + Doi = {10.1021/acs.jproteome.5b00354}, + Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354} +}</citation> + +</citations> + +Input files +=========== + +| **To generate the "dataMatrix":** +| **1) copy/paste the values below in a .txt files** +| **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:** +| **Set the option 'Convert spaces to tabs' to 'Yes'** +| + +**dataMatrix file**:: + + dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209 + HMDB01032 2569204.92420381 0 NA 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 NA 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586 + HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 0 8932005.5351622 8340827.52597275 NA 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067 + HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 NA 474901.604069803 0 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275 + + +</tool> |
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| diff -r 000000000000 -r eacea1349a7c transformation_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transformation_script.R Fri Jul 29 12:11:01 2016 -0400 |
| [ |
| @@ -0,0 +1,85 @@ +## Etienne Thevenot +## W4M Core Development Team +## etienne.thevenot@cea.fr +## 2015-04-25 + +transformF <- function(datMN, + metC) { + + ## options + + optStrAsFacL <- options()[["stringsAsFactors"]] + options(stringsAsFactors = FALSE) + + ## transformation + + switch(metC, + log2 = { + + cat("\n'log2' transformation\n", sep="") + + if(length(which(datMN < 0))) + stop("The 'dataMatrix' contains negative values") + + zerMN <- datMN == 0 + + ## Number of missing values + nasN <- length(which(is.na(datMN))) + cat("\nMissing values in the 'dataMatrix': ", + nasN, + " (", + round(nasN / cumprod(dim(datMN))[2] * 100), + "%)\n", + sep="") + + ## Number of zero values + zerN <- length(which(zerMN)) + cat("\nZero values in the 'dataMatrix': ", + zerN, + " (", + round(zerN / cumprod(dim(datMN))[2] * 100), + "%)\n", + sep="") + + trfMN <- log2(1 + datMN) + + }, + log10 = { + + cat("\n'log10' transformation\n", sep="") + + if(length(which(datMN < 0))) + stop("The 'dataMatrix' contains negative values") + + zerMN <- datMN == 0 + + ## Number of missing values + nasN <- length(which(is.na(datMN))) + cat("\nMissing values in the 'dataMatrix': ", + nasN, + " (", + round(nasN / cumprod(dim(datMN))[2] * 100), + "%)\n", + sep="") + + ## Number of zero values + zerN <- length(which(zerMN)) + cat("\nZero values in the 'dataMatrix': ", + zerN, + " (", + round(zerN / cumprod(dim(datMN))[2] * 100), + "%)\n", + sep="") + + trfMN <- log10(1 + datMN) + + }) ## end of 'log10' method + + + ## returning + + options(stringsAsFactors=optStrAsFacL) + + return(trfMN) + +} ## end of transformF |
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| diff -r 000000000000 -r eacea1349a7c transformation_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transformation_wrapper.R Fri Jul 29 12:11:01 2016 -0400 |
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| @@ -0,0 +1,126 @@ +#!/usr/bin/Rscript --vanilla --slave --no-site-file + + +library(batch) ## parseCommandArgs + +source_local <- function(fname){ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +source_local("transformation_script.R") + +argVc <- unlist(parseCommandArgs(evaluate=FALSE)) + + +#### Start_of_tested_code <- function() {} + + +##------------------------------ +## Initializing +##------------------------------ + +## options +##-------- + +strAsFacL <- options()[["stringsAsFactors"]] +options(stringsAsFactors=FALSE) + +## constants +##---------- + +modNamC <- "Transformation" ## module name +metVc <- c("log2", "log10") ## available methods + +topEnvC <- environment() +flagC <- "\n" + +## functions +##---------- + +flgF <- function(tesC, + envC = topEnvC, + txtC = NA) { ## management of warning and error messages + + tesL <- eval(parse(text = tesC), envir = envC) + + if(!tesL) { + + sink(NULL) + stpTxtC <- ifelse(is.na(txtC), + paste0(tesC, " is FALSE"), + txtC) + + stop(stpTxtC, + call. = FALSE) + + } + +} ## flgF + +## log file +##--------- + +sink(argVc[["information"]]) + +cat("\nStart of the '", modNamC, "' module: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") + +## loading +##-------- + +datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]], + check.names = FALSE, + header = TRUE, + row.names = 1, + sep = "\t"))) + +metC <- argVc[["method"]] + +## checking +##--------- + +flgF("metC %in% metVc", txtC = paste0("Transformation method must be either '", paste(metVc, collapse = "', '"), "'")) + + +##------------------------------ +## Computation +##------------------------------ + + +datMN <- transformF(datMN = datMN, ## dataMatrix + metC = metC) ## transformation method + + +##------------------------------ +## Ending +##------------------------------ + + +## saving +##------- + +datDF <- cbind.data.frame(dataMatrix = colnames(datMN), + as.data.frame(t(datMN))) +write.table(datDF, + file = argVc[["dataMatrix_out"]], + quote = FALSE, + row.names = FALSE, + sep = "\t") + +## ending +##------- + +cat("\nEnd of the '", modNamC, "' Galaxy module call: ", + format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "") + +sink() + +options(stringsAsFactors = strAsFacL) + + +#### End_of_tested_code <- function() {} + + +rm(list = ls()) |
