| Previous changeset 5:3d00a98974b7 (2018-10-02) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136 |
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modified:
NmrNormalization_script.R NmrNormalization_wrapper.R NmrNormalization_xml.xml README.rst test-data/MTBLS1_bucketedData_normalized.tabular |
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added:
test-data/MTBLS1_bucketedData.tabular.tsv test-normalization.sh |
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removed:
MANUAL_INSTALL.txt test-data/MTBLS1_bucketedData.tabular |
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| diff -r 3d00a98974b7 -r 221cbd549c40 MANUAL_INSTALL.txt --- a/MANUAL_INSTALL.txt Tue Oct 02 12:14:47 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,44 +0,0 @@ -Instructions to integrate the NMR Normalization" tool into a local instance of Galaxy -Version mars 2015 M Tremblay-Franco - - -## --- R bin and Packages : --- ## -R version 3.0.2 (2013-09-25) -- "Frisbee Sailing -Platform: x86_64-redhat-linux-gnu (64-bit) - -Install the "batch" library, necessary for parseCommandArgs function: - - Download package source (*.tar.gz file) from your favorite CRAN (http://www.r-project.org/) -For example: http://cran.univ-lyon1.fr/ - - - Install package in your R session -install.packages("path/package_name.tar.gz",lib="path",repos=NULL) -For Example: install.packages("/usr/lib64/R/library/batch_1.1-4.tar",lib="/usr/lib64/R/library",repos=NULL) - - - Finally, load the package into your R session -library(batch) - - - -## --- Config : --- ## - - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add -<section id="id_name" name="Name"> - <tool file="path/NmrNormalization_xml.xml" /> -</section> -to create a new section containing the Nmr_Normalization tool -or add - <tool file="path/NmrNormalization_xml.xml" /> -in an existing section - - - Put the three files NmrNormalization_xml.xml, NmrNormalization_wrapper.R and NmrNormalization_script.R in a same directory -For example, path=/galaxy/dist/galaxy-dist/tools/stats - - - Edit the NmrBucketing_xml.xml file and change the path in the following lines - # R script - R --vanilla --slave --no-site-file --file=path/NmrNormalization_wrapper.R --args - - ## Library name for raw files storage - library path/$library - - - -Finally, restart Galaxy |
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| diff -r 3d00a98974b7 -r 221cbd549c40 NmrNormalization_script.R --- a/NmrNormalization_script.R Tue Oct 02 12:14:47 2018 -0400 +++ b/NmrNormalization_script.R Tue Jul 30 09:43:57 2019 -0400 |
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| @@ -96,12 +96,22 @@ # Recuperation spectres individus controle control.spectra <- data.normalized[,sampleMetadata[,pqnFactor]==nomControl] spectrum.ref <- apply(control.spectra,1,median) + for (j in 1:length(spectrum.ref)) + { + if (spectrum.ref[j] == 0) + spectrum.ref[j] <- mean(control.spectra[j, ]) + if (spectrum.ref[j] == 0) + spectrum.ref[j] <- 10^(-24) + } # Ratio between normalized and reference spectra data.normalized.ref <- data.normalized/spectrum.ref # Median ratio data.normalized.ref.median <- apply(data.normalized.ref,1,median) + for (j in 1:length(data.normalized.ref.median)) + if (data.normalized.ref.median[j] == 0 | is.na(data.normalized.ref.median[j]) | data.normalized.ref.median == "NaN" | data.normalized.ref.median == "NA") + data.normalized.ref.median[j] <- mean(data.normalized.ref[j, ]) # Normalization data.normalizedPQN <- data.normalized[,1]/data.normalized.ref.median @@ -145,3 +155,4 @@ return(list(NormalizedBucketedSpectra)) } + |
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| diff -r 3d00a98974b7 -r 221cbd549c40 NmrNormalization_wrapper.R --- a/NmrNormalization_wrapper.R Tue Oct 02 12:14:47 2018 -0400 +++ b/NmrNormalization_wrapper.R Tue Jul 30 09:43:57 2019 -0400 |
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| @@ -14,6 +14,7 @@ ##------------------------------ strAsFacL <- options()$stringsAsFactors options(stringsAsFactors = FALSE) +options(scipen=999) ##------------------------------ |
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| diff -r 3d00a98974b7 -r 221cbd549c40 NmrNormalization_xml.xml --- a/NmrNormalization_xml.xml Tue Oct 02 12:14:47 2018 -0400 +++ b/NmrNormalization_xml.xml Tue Jul 30 09:43:57 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="normalization" name="Normalization" version="1.0.6"> +<tool id="normalization" name="Normalization" version="1.0.7"> <description> Normalization of (preprocessed) spectra </description> @@ -86,7 +86,7 @@ <tests> <test> - <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" /> + <param name="dataMatrix" value="MTBLS1_bucketedData.tabular.tsv" ftype="tabular" /> <conditional name="scalingMethod" > <param name="method" value="Total" /> </conditional> @@ -99,8 +99,8 @@ .. class:: infomark -**Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) and Marion Landi (marion.landi@clermont.inra.fr) - MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en) +**Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr) and Marion Landi (marion.landi@clermont.inra.fr) + MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (https://www.metabohub.fr/home.html) --------------------------------------------------- @@ -240,11 +240,14 @@ -------------- Changelog/News -------------- +**Version 1.0.7 - 25/09/2018** + +- Bug fixing for PQN normalization in case of zero's **Version 1.0.3 - 30/01/2017** - BUGFIX: Fix a bug: stack overflow for integers - + **Version 1.0.2 - 22/10/2016** - NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data |
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| diff -r 3d00a98974b7 -r 221cbd549c40 README.rst --- a/README.rst Tue Oct 02 12:14:47 2018 -0400 +++ b/README.rst Tue Jul 30 09:43:57 2019 -0400 |
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| @@ -13,10 +13,3 @@ **Version 2015-01-28 - 28/01/2015** - -Test Status ------------ - -Planemo test using conda: passed - -Planemo shed_test: passed |
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| diff -r 3d00a98974b7 -r 221cbd549c40 test-data/MTBLS1_bucketedData.tabular --- a/test-data/MTBLS1_bucketedData.tabular Tue Oct 02 12:14:47 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 3d00a98974b7 -r 221cbd549c40 test-data/MTBLS1_bucketedData.tabular.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_bucketedData.tabular.tsv Tue Jul 30 09:43:57 2019 -0400 |
| b |
| b'@@ -0,0 +1,654 @@\n+Bucket\tADG10003u_007\tADG10003u_008\tADG10003u_009\tADG10003u_010\tADG10003u_015\tADG10003u_016\tADG10003u_017\tADG10003u_021\tADG10003u_022\tADG10003u_023\tADG10003u_051\tADG10003u_052\tADG10003u_053\tADG10003u_066\tADG10003u_067\tADG10003u_071\tADG10003u_072\tADG10003u_073\tADG10003u_087\tADG10003u_088\tADG10003u_089\tADG10003u_097\tADG10003u_098\n+B9.295\t1.79949423217956e-06\t1.36845276225836e-05\t2.01160697683997e-05\t7.25986492795804e-07\t2.42490464839257e-05\t3.11580892214512e-05\t8.19866824235026e-06\t3.09192259268499e-05\t2.64389193821353e-05\t1.45055826888266e-05\t3.45040700032625e-06\t1.60970199365859e-05\t1.05993065753594e-05\t2.90248760646802e-05\t1.06130409475137e-05\t5.2278556041205e-06\t2.44519080406605e-05\t3.7420635381202e-05\t1.57230624459948e-05\t2.75224138622866e-06\t2.08828714579133e-05\t5.49917968773367e-05\t8.22464110337308e-06\n+B9.286\t0.000183987136571742\t4.73741598311689e-05\t6.48220850387143e-05\t4.08486623139604e-05\t0.000124595459054319\t3.41874426311483e-05\t0.000122371178407348\t3.49547713922308e-05\t0.00015628757744243\t2.37737814473545e-05\t5.13987818577577e-05\t0.000134108924379129\t9.59219627606648e-05\t8.44451844992086e-05\t0.00022720535031565\t9.86157895513715e-05\t1.06199525078497e-05\t3.70983827911379e-05\t3.16119098225048e-05\t5.1709215131723e-06\t2.21703993321988e-05\t1.19479684646357e-05\t8.95607890845055e-06\n+B9.276\t6.1185692617288e-05\t0.00020732837726723\t0.00012538786536446\t2.84181782334477e-05\t2.53083682825459e-05\t2.76930477756038e-05\t9.7914592965261e-05\t1.44908072132008e-05\t7.76504143484867e-05\t2.21918164602678e-05\t0.000443221195814841\t0.00034996670727668\t0.000412632862820386\t0.000146364982064243\t0.000101892447453022\t0.00020898968160112\t0.00018589786110267\t0.000307514987819811\t0.000357112398084273\t0.000316352014982079\t0.00021198645013364\t0.000691068949900525\t0.000221146831632783\n+B9.266\t4.50617404358542e-05\t7.7187909059995e-06\t1.52411037411529e-05\t1.10253427920853e-05\t4.1745051441984e-05\t3.63488304424524e-05\t3.3290398209022e-05\t1.13169550474572e-05\t9.45184418976979e-06\t7.6012521812347e-06\t6.92482995870393e-06\t3.8268420757911e-05\t2.37195119946984e-06\t2.86004474506151e-05\t3.22860579421692e-06\t2.96039906990133e-06\t2.52808779783966e-05\t0.000142090898957934\t1.10312630129144e-05\t3.60677293639806e-06\t2.97265975382987e-05\t6.66305467846902e-06\t1.14495101906091e-05\n+B9.255\t1.15660880406503e-05\t2.14664012391468e-05\t4.60009639329725e-06\t1.25395676678615e-05\t4.17248489153109e-05\t1.46532714803481e-05\t1.00057270405122e-05\t2.75328532847705e-05\t2.74077840472564e-05\t2.41894891121703e-06\t8.0400281246103e-06\t1.59037103857697e-05\t1.00611731499731e-06\t6.71681516896861e-06\t1.36105357122668e-05\t7.11442411954162e-06\t2.21537557041547e-05\t2.87845824558775e-05\t4.03717597605331e-05\t1.42618582461408e-05\t1.84330229833385e-05\t6.39363012853215e-05\t2.18920831381193e-05\n+B9.246\t2.03293920474837e-07\t2.02423815996018e-05\t4.96598896737477e-06\t1.35705313106542e-05\t3.41075710581766e-05\t6.53017072634504e-05\t4.43984949390479e-06\t1.63183767828055e-05\t2.72484433555238e-06\t8.78724169594538e-06\t8.95623692386308e-07\t2.45735590368271e-05\t5.26105502709834e-06\t2.37539064007069e-05\t2.19035721346259e-05\t1.50517785846819e-05\t2.16082826646081e-05\t2.53649297518041e-05\t1.32773972605395e-05\t1.00977058894297e-05\t1.55783781762885e-05\t3.76630403674761e-05\t2.14582962168246e-05\n+B9.236\t3.37742336734625e-05\t1.09466424044581e-05\t1.26844396116922e-05\t1.41040509503652e-05\t8.32806751647478e-06\t6.89331798338183e-05\t1.31306116922384e-05\t2.44043814312157e-05\t2.60353424850613e-06\t1.5498729364209e-05\t1.12441000124573e-05\t1.90904945628191e-05\t4.77289113406423e-06\t2.6783614160707e-05\t1.81281101162131e-05\t2.27290178082349e-05\t2.2060579242685e-05\t2.02102446881195e-05\t2.82836945109232e-05\t2.6769889759727e-05\t3.20529608453921e-05\t1.46895321061598e-05\t2.72459848898296e-05\n+B9.226\t1.02347475703096e-05\t1.61525191983677e-05\t6.32740402153627e-06\t2.17291460045977e-06\t3.58860102752402e-05\t5.32064617047859e-05\t3.88074184844747e-06\t1.41925328605111e-05\t3.61825110992116e-05\t1.56626397248238e-05\t1.48898939857621e-0'..b'5755e-05\t1.07484288284833e-06\t2.0921264303262e-05\t3.39206429967707e-05\t1.70346084887867e-06\n+B0.27\t4.65219901950512e-05\t1.10152209572177e-05\t9.65137843945446e-06\t1.84242750160577e-05\t2.39463170195535e-05\t6.99870162577904e-05\t3.87147657316298e-05\t4.1016025818645e-05\t2.68562864134689e-06\t4.15420761297383e-05\t1.04910281852965e-05\t2.92481867818242e-05\t3.29030151532543e-06\t1.6989691539782e-05\t4.30775393958073e-05\t1.3432166774511e-05\t4.03008033378747e-05\t4.59937298032909e-05\t4.64750012890975e-06\t7.73657900389351e-06\t2.39771929723297e-05\t1.41885650306241e-06\t9.92898214215284e-06\n+B0.26\t3.89797135271624e-06\t3.18199705844843e-05\t3.03011438640063e-06\t1.03880700020792e-05\t1.70193178595592e-05\t6.45781752331893e-05\t3.58594763822763e-06\t1.16904371476316e-05\t1.17039454862549e-05\t3.6618470378685e-05\t3.25536311251976e-06\t2.00477250599857e-05\t5.20547993823536e-06\t2.27239699572945e-07\t2.08950497409999e-05\t2.69789629711028e-05\t1.87211348640047e-05\t4.42851467969171e-05\t2.37708102730504e-05\t1.88870553860999e-05\t2.707516130055e-05\t2.97998380410034e-05\t1.5496183245749e-05\n+B0.25\t3.36113818828055e-05\t2.11189684317557e-05\t3.33117767218542e-06\t5.36908274723988e-06\t2.69299680369503e-05\t6.01665567664201e-05\t2.38349757020467e-05\t4.49372682910286e-05\t1.42970293986657e-05\t5.22366824060723e-05\t7.35557332042657e-06\t3.00546471230146e-05\t6.67509669761163e-06\t1.9458657846185e-06\t2.07207784055168e-06\t1.3962170777214e-06\t2.6493254026595e-05\t4.06091388230294e-05\t1.18049669263359e-05\t1.68343231094999e-05\t3.60850200098749e-05\t4.59439903623729e-06\t2.24900254753656e-05\n+B0.239\t3.89114674330758e-05\t2.34306869291169e-05\t1.16440605028436e-05\t1.11904911551342e-05\t3.69704695689001e-05\t8.38227971529335e-05\t2.92968664891787e-05\t5.30555504854832e-05\t2.32923985983179e-07\t1.07811615997015e-05\t2.86819156038087e-07\t2.19132469275404e-05\t2.70956586041059e-06\t1.69111567560848e-05\t8.88325202185832e-06\t1.17925890601426e-05\t3.45093151766689e-05\t5.07214951782308e-05\t1.50789432007085e-05\t1.40750680666096e-05\t2.085552035437e-05\t6.67499425621024e-05\t1.84624232013409e-05\n+B0.228\t2.71512932782877e-05\t7.22512090595987e-06\t4.00877470310617e-06\t2.52691273430091e-06\t1.34154030083913e-06\t4.44031760433474e-05\t8.50182540888497e-06\t1.79456764298474e-05\t1.24176926680955e-05\t3.54471286879102e-05\t8.50559462549758e-06\t1.67062179513423e-05\t2.84538048682202e-06\t2.68181570734585e-05\t1.38609638993149e-05\t4.34861582375874e-05\t2.28148877835839e-05\t5.365262606744e-05\t3.64439699333137e-05\t2.33877601203837e-05\t3.85265618530103e-05\t8.20352155809884e-05\t5.94274879332494e-06\n+B0.219\t1.75580228833559e-06\t4.40647070234501e-06\t5.64587794282773e-06\t2.5787607535262e-05\t1.29478147577712e-05\t5.26793729691012e-05\t3.64311284622012e-05\t3.91629964025322e-05\t1.79773792067952e-05\t2.48598994351104e-05\t1.45811173823145e-08\t1.27901466715041e-05\t1.72969856577897e-05\t2.83651529014306e-05\t1.2472769026795e-05\t1.7960378000977e-05\t3.98713500213186e-05\t5.04990493356441e-05\t2.62912075256493e-06\t5.67074769206449e-06\t2.58766764633525e-05\t5.51088542582568e-05\t1.46880222212507e-05\n+B0.208\t2.14485918819516e-05\t7.76849243554768e-06\t3.67447822155504e-06\t1.25085369091504e-05\t1.85332736169264e-05\t5.53378373460843e-05\t1.40329306634423e-05\t6.30720293551732e-05\t7.51131373855451e-07\t2.54944770646103e-05\t6.34192834852026e-07\t7.58085896637617e-07\t7.55004399016523e-06\t2.63494267865413e-05\t3.07372110250848e-05\t1.10287186969214e-05\t1.52499209346627e-05\t4.47864411627061e-05\t1.87033871002537e-05\t6.09517706188692e-06\t1.65915846120559e-05\t1.23369676105833e-05\t1.19506316390872e-05\n+B0.201\t7.94940614451578e-07\t8.39071735333468e-06\t3.36768507443121e-06\t8.36212316677346e-06\t6.69783156750708e-06\t1.32981196904848e-05\t1.46316523125031e-05\t2.12410753943458e-05\t1.35059281826271e-05\t3.21513682981475e-06\t1.78335642713577e-06\t9.10088942157247e-06\t2.94179605887352e-06\t7.99459313882706e-06\t6.39064382949492e-06\t9.79697599095551e-06\t8.68043937719882e-07\t1.33709392799666e-05\t1.13251600585399e-06\t2.31337213505483e-06\t2.36040023595129e-06\t2.0192742089148e-06\t4.00266356025354e-06\n' |
| b |
| diff -r 3d00a98974b7 -r 221cbd549c40 test-data/MTBLS1_bucketedData_normalized.tabular --- a/test-data/MTBLS1_bucketedData_normalized.tabular Tue Oct 02 12:14:47 2018 -0400 +++ b/test-data/MTBLS1_bucketedData_normalized.tabular Tue Jul 30 09:43:57 2019 -0400 |
| b |
| b'@@ -1,595 +1,654 @@\n Variable\tADG10003u_007\tADG10003u_008\tADG10003u_009\tADG10003u_010\tADG10003u_015\tADG10003u_016\tADG10003u_017\tADG10003u_021\tADG10003u_022\tADG10003u_023\tADG10003u_051\tADG10003u_052\tADG10003u_053\tADG10003u_066\tADG10003u_067\tADG10003u_071\tADG10003u_072\tADG10003u_073\tADG10003u_087\tADG10003u_088\tADG10003u_089\tADG10003u_097\tADG10003u_098\n-B9.295\t1.28208230777605e-06\t6.03679847460637e-06\t1.10247640127855e-05\t8.94265805369699e-07\t2.14167917232182e-05\t2.52495960990511e-05\t4.76262934896432e-06\t7.44250073104011e-05\t2.45076064436471e-05\t7.07853640602565e-05\t1.85585745682456e-06\t8.00757207754199e-06\t5.97768909757741e-06\t1.7072118430662e-05\t1.09625352509915e-05\t2.00116485731369e-06\t9.13645217196289e-06\t1.15122771587968e-05\t5.99631364379717e-06\t1.10084198597185e-06\t8.31398031738169e-06\t2.07802091664521e-05\t2.63590723864643e-06\n-B9.286\t0.000131084972898912\t2.08986574978731e-05\t3.55262334340865e-05\t5.03171371161353e-05\t0.000110042883459108\t2.77044947127785e-05\t7.10857603360121e-05\t8.41388824725089e-05\t0.000144871066197137\t0.000116012973138695\t2.76456697929837e-05\t6.67133967925786e-05\t5.40970927612979e-05\t4.96697449269704e-05\t0.000234687369469982\t3.77490251014015e-05\t3.96814383544791e-06\t1.14131377108915e-05\t1.20558527848026e-05\t2.06826608172814e-06\t8.82657655810766e-06\t4.51487854385105e-06\t2.87032503035197e-06\n-B9.276\t4.35928565876175e-05\t9.146093063263e-05\t6.87197669139952e-05\t3.50053414178626e-05\t2.23523862153131e-05\t2.24416287570138e-05\t5.68788613423108e-05\t3.48805120583418e-05\t7.19781987884388e-05\t0.000108293188973956\t0.000238393720276448\t0.000174093319403096\t0.00023271248433532\t8.6090300690144e-05\t0.000105247831657074\t7.99989207872733e-05\t6.94607109600787e-05\t9.46054959837503e-05\t0.000136192166911309\t0.000126534533701012\t8.43969746935755e-05\t0.000261139990740902\t7.08751332706188e-05\n-B9.266\t3.21050543743229e-05\t3.40507078156242e-06\t8.35300205135251e-06\t1.35809510910754e-05\t3.68692877388251e-05\t2.94560196173053e-05\t1.93384855762315e-05\t2.72408004046139e-05\t8.76140489032508e-06\t3.70931257643979e-05\t3.7246322868252e-06\t1.90368862509883e-05\t1.33770890805428e-06\t1.68224741066507e-05\t3.33492587145347e-06\t1.13320776833264e-06\t9.44619667842539e-06\t4.37135765836851e-05\t4.20699931326061e-06\t1.44263766329546e-06\t1.18348833077977e-05\t2.5178240713781e-06\t3.66944240010732e-06\n-B9.255\t8.24046922847721e-06\t9.46969759057739e-06\t2.52111758191632e-06\t1.54461642065868e-05\t3.68514448390506e-05\t1.18745788221766e-05\t5.81235486694224e-06\t6.62737421642824e-05\t2.54056973817355e-05\t1.18041572680532e-05\t4.32445973669958e-06\t7.91140892637885e-06\t5.67419808266028e-07\t3.95075809405572e-06\t1.40587394572861e-05\t2.7233222579503e-06\t8.27774785852221e-06\t8.85543732105539e-06\t1.53966019474694e-05\t5.70446052947563e-06\t7.33863590465418e-06\t2.41601436847361e-05\t7.01617246120952e-06\n-B9.246\t1.44840441307517e-07\t8.92973303376659e-06\t2.7216477714453e-06\t1.67160990352341e-05\t3.01238543965865e-05\t5.29185766579494e-05\t2.57912100838876e-06\t3.92796156743214e-05\t2.5257996225459e-06\t4.28806009297429e-05\t4.81725752314645e-07\t1.22242841199376e-05\t2.96707629443903e-06\t1.39717910374546e-05\t2.26248709334081e-05\t5.76165308008723e-06\t8.07393193018543e-06\t7.80339773607554e-06\t5.06360886251959e-06\t4.03888214918222e-06\t6.2021322017625e-06\t1.42320473438326e-05\t6.87714851213995e-06\n-B9.236\t2.40630654308869e-05\t4.82900659721989e-06\t6.95180295969216e-06\t1.73732853259174e-05\t7.35536086235275e-06\t5.58614148722852e-05\t7.62760911488983e-06\t5.87432644892573e-05\t2.41335100738113e-06\t7.56317911559655e-05\t6.04782185157489e-06\t9.49669639535279e-06\t2.69176658804703e-06\t1.57538323999657e-05\t1.87250805085604e-05\t8.70041468690272e-06\t8.24293248614493e-06\t6.21758385250751e-06\t1.07865693388531e-05\t1.07074251389435e-05\t1.27610652643947e-05\t5.55085607411956e-06\t8.7320392333836e-06\n-B9.226\t7.2919315604333e-06\t7.1255293530802e-06\t3.46778157732234e-06\t2.67658316575083e-06\t3.1694574397041e-05\t4.31169465610414e-05\t2.2543338109107e-06\t3.41625422446099e-05\t3.35394472574981e-05\t7.64316524782069e-05\t8.008771'..b'08\t0.000201070024307191\t0.00000561724759240202\t0.0000144895828317177\t0.00000185141932013468\t0.00000996924861327926\t0.0000443451003612899\t0.00000512221704727725\t0.0000150022761860313\t0.0000140753126148567\t0.00000176654853934501\t0.00000308472821545925\t0.00000951071732017676\t0.000000533691037822423\t0.00000316433190354458\n+B0.26\t0.0000027674618880512\t0.0000139826184245575\t0.00000165316979126797\t0.0000127556991584955\t0.000014961786731862\t0.0000520002041621626\t0.00000207319378347167\t0.0000279104793939977\t0.0000108180611261197\t0.000177239016801656\t0.00000174303035729373\t0.00000993166431174056\t0.00000292907081108925\t0.000000133340211300778\t0.0000215098886987256\t0.0000102881468320271\t0.00000696908280936888\t0.0000135524404745454\t0.00000903545755828853\t0.00000753064534429537\t0.0000107395476119697\t0.0000112089604951007\t0.00000493857943600497\n+B0.25\t0.0000238632380662779\t0.0000092802875576983\t0.00000181742389717006\t0.00000659279387481532\t0.0000236743000976624\t0.0000484478420811779\t0.0000137800460129152\t0.000107286039420125\t0.0000132148716976113\t0.000252833560082885\t0.00000393842012385509\t0.0000148891041422639\t0.00000375600926910891\t0.00000114179940992528\t0.0000021330489411522\t0.000000532432855939174\t0.00000986231243683752\t0.0000124274836243734\t0.00000448715363147864\t0.00000671218008087271\t0.0000143133695926332\t0.00000172814487196382\t0.00000716749250873356\n+B0.239\t0.0000276261658655196\t0.0000102961237467284\t0.00000635276646894626\t0.0000137410066145229\t0.0000325009665858019\t0.0000674965272656995\t0.0000169378049007388\t0.000126668133095629\t0.000000215293716214306\t0.0000521824768252233\t0.000000153572575085422\t0.0000108558458285624\t0.00000152464525204626\t0.00000992316579996659\t0.00000914464261350728\t0.00000449698114454781\t0.0000128463512980308\t0.0000155221353862774\t0.00000573161578208\t0.00000561201011166947\t0.00000827248455999449\t0.0000251074340806602\t0.00000588390974183761\n+B0.228\t0.0000192767371947466\t0.00000317492778414419\t0.0000021871072817969\t0.00000310284187843\t0.00000117935630787219\t0.0000357547145202678\t0.00000491527857182362\t0.0000428446281247985\t0.0000114777840076741\t0.000171569543241871\t0.00000455418001821654\t0.00000827627813704784\t0.00000160106676603937\t0.0000157364172615645\t0.0000142688241677787\t0.0000165829940012247\t0.00000849301302539961\t0.0000164191399074835\t0.000013852617550918\t0.00000932516600727953\t0.0000152818238367243\t0.0000308568620201603\t0.00000189393326851043\n+B0.219\t0.00000124657558412681\t0.00000193633109327655\t0.00000308027805886102\t0.0000316650699958044\t0.0000113825033792773\t0.0000424189463334374\t0.0000210624350025434\t0.0000935001822683361\t0.0000166166518269366\t0.000120325728740208\t0.00000000780721823101484\t0.00000633625226100318\t0.00000973283854922245\t0.0000166441668800109\t0.0000128397815203494\t0.00000684900328565916\t0.0000148424089692425\t0.0000154540610033632\t0.000000999347885181181\t0.00000226104010566665\t0.0000102641604174696\t0.0000207287358226951\t0.00000468102134229419\n+B0.208\t0.0000152279622435662\t0.00000341370100176304\t0.00000200472180912041\t0.0000153594588498272\t0.0000162927145252153\t0.0000445596183152915\t0.00000811305338237367\t0.000150582100004004\t0.000000694277423425924\t0.000123397181861373\t0.000000339568068236056\t0.000000375556559277506\t0.00000424833324427902\t0.0000154613746716558\t0.0000316416565767495\t0.00000420568712906356\t0.00000567689739975828\t0.0000137058499705946\t0.00000710929322136638\t0.00000243026855300777\t0.00000658116533161997\t0.0000046404474543147\t0.00000380862453186702\n+B0.201\t0.000000564387896854535\t0.00000368712468631886\t0.00000183734160549859\t0.0000102680023739057\t0.00000588810481747293\t0.0000107080284690778\t0.00000845920065670371\t0.0000507122693200868\t0.0000124836497928183\t0.0000155617557125176\t0.000000954868714466231\t0.00000450859029654874\t0.00000165531883139768\t0.00000469108496621983\t0.00000657868917229271\t0.00000373597486355399\t0.000000323135863722229\t0.00000409186537218668\t0.00000043047755576836\t0.000000922387568752225\t0.00000093626887152796\t0.000000759533149319744\t0.00000127563488598635\n' |
| b |
| diff -r 3d00a98974b7 -r 221cbd549c40 test-normalization.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-normalization.sh Tue Jul 30 09:43:57 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ +#!/bin/bash + +# Variables +script_dir="${0%/*}" +normalization_script=$script_dir/galaxy/normalization/NmrNormalization_wrapper.R +data_dir=$script_dir/galaxy/normalization/test-data + +# Run script +Rscript $normalization_script dataMatrix $data_dir/MTBLS1_bucketedData.tabular scalingMethod Total graphType Overlay logOut norm.log dataMatrixOut $script_dir/matrixout.tabular || exit 1 + +# Test output file +diff $data_dir/MTBLS1_bucketedData_normalized.tabular $script_dir/matrixout.tabular || exit 2 |