| Next changeset 1:f9554d5bb47e (2017-03-02) |
|
Commit message:
Uploaded |
|
added:
normalization/.shed.yml normalization/DrawSpec.R normalization/MANUAL_INSTALL.txt normalization/NmrNormalization_script.R normalization/NmrNormalization_wrapper.R normalization/NmrNormalization_xml.xml normalization/README.rst normalization/planemo_test.sh normalization/test-data/MTBLS1_bucketedData.tabular normalization/test-data/MTBLS1_bucketedData_normalized.tabular normalization/tool_dependencies.xml |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/.shed.yml Thu Mar 02 10:27:05 2017 -0500 |
| [ |
| @@ -0,0 +1,7 @@ +categories: [Metabolomics] +description: '[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data' +homepage_url: http://workflow4metabolomics.org +long_description: 'Part of the W4M project: http://workflow4metabolomics.org' +name: normalization +owner: marie-tremblay-metatoul +remote_repository_url: https://github.com/workflow4metabolomics/normalization |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/DrawSpec.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/DrawSpec.R Thu Mar 02 10:27:05 2017 -0500 |
| [ |
| @@ -0,0 +1,74 @@ +drawSpec <- function (X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1, + xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0) +{ + groupLabel_name = groupLabel + X = as.data.frame(X) +# colnames(X) = c(1:ncol(X)) + X = as.matrix(X) + if (highBound != -1) { + for (i in 1:nrow(X)) { + myIndex = which(X[i, ] > highBound) + X[i, myIndex] = highBound + } + } + if (lowBound != -1) { + for (i in 1:nrow(X)) { + myIndex = which(X[i, ] < lowBound) + X[i, myIndex] = lowBound + } + } + if (is.null(groupLabel)) { + groupLabel = c(1:nrow(X)) + groupLabel = as.factor(groupLabel) + } + else { + levels(groupLabel) = c(1:length(levels(groupLabel))) + } + if (startP == -1) + startP = 1 + if (endP == -1) + endP = ncol(X) + if (is.null(xlab)) { + xlab = "index" + } + if (is.null(ylab)) { + ylab = "intensity" + } + if (is.null(main)) { + main = paste(" ", startP + offside, "-", endP + offside) + } + GraphRange <- c(startP:endP) + yn <- X[, GraphRange] + if (useLog != -1) + yn = log(yn) + if (length(yn) > ncol(X)) + { + plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n") + tempVal = trunc(length(GraphRange)/nAxisPos) + xPos = c(0:nAxisPos) * tempVal + axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside]) + for (i in 1:length(levels(groupLabel))) + { + groupLabelIdx = which(groupLabel == levels(groupLabel)[i]) + color <- palette(rainbow(length(levels(groupLabel)))) + for (j in 1:length(groupLabelIdx)) + { + lines(yn[groupLabelIdx[j], ], col = color[i]) + } + } + if (!is.null(groupLabel_name)) + { + legendPos = "topleft" + legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90") + } + } + if (length(yn) == ncol(X)) + { + plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n") + tempVal = trunc(length(GraphRange)/nAxisPos) + xPos = c(0:nAxisPos) * tempVal +# axis(1, at = xPos, labels = xPos + startP + offside) + axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside]) + lines(yn) + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/MANUAL_INSTALL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/MANUAL_INSTALL.txt Thu Mar 02 10:27:05 2017 -0500 |
| b |
| @@ -0,0 +1,44 @@ +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/$library + + + +Finally, restart Galaxy |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/NmrNormalization_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/NmrNormalization_script.R Thu Mar 02 10:27:05 2017 -0500 |
| [ |
| @@ -0,0 +1,147 @@ +################################################################################################################# +# SPECTRA NORMALIZATION FROM SPECTRAL DATA # +# User : Galaxy # +# Original data : -- # +# Starting date : 20-10-2014 # +# Version 1 : 27-01-2015 # +# Version 2 : 27-02-2015 # +# # +# Input files: # +# - Data matrix containing bucketed and integrated spectra to normalize # +# - Sample metadata matrix containing at least biological factor of interest # +# - Scaling method: Total intensity/Probabilistic Quotient Normalization # +# - Control group: name of control to compute median reference spectra # +# - Graph: normalization result representation # +################################################################################################################# +NmrNormalization <- function(dataMatrix,scalingMethod=c("None","Total","PQN","BioFactor"),sampleMetadata=NULL, + bioFactor=NULL,ControlGroup=NULL,graph=c("None","Overlay","One_per_individual"), + nomFichier=NULL,savLog.txtC=NULL) +{ + + ## Option + ##--------------- + strAsFacL <- options()$stringsAsFactors + options(stingsAsFactors = FALSE) + options(warn = -1) + + + ## Constants + ##--------------- + topEnvC <- environment() + flgC <- "\n" + + ## Log file (in case of integration into Galaxy) + ##---------------------------------------------- + if(!is.null(savLog.txtC)) + sink(savLog.txtC, append = TRUE) + + ## Functions definition + ##--------------------- + ################################################################################################################# + # Total intensity normalization + # Input parameters + # - data : bucketed spectra (rows=buckets; columns=samples) + ################################################################################################################# + NmrBrucker_total <- function(data) + { + # Total intensity normalization + data.total <- apply(data,2,sum) + data.normalized <- data[,1]/data.total[1] + for (i in 2:ncol(data)) + data.normalized <- cbind(data.normalized,data[,i]/data.total[i]) + colnames(data.normalized) <- colnames(data) + rownames(data.normalized) <- rownames(data) + return(data.normalized) + } + + + ################################################################################################################# + # Biological factor normalization + # Input parameters + # - data : bucketed spectra (rows=buckets; columns=samples) + # - sampleMetadata : dataframe with biological factor of interest measured for each invidual + # - bioFactor : name of the column cotaining the biological factor of interest + ################################################################################################################# + NmrBrucker_bioFact <- function(data,sampleMetadata,bioFactor) + { + # Total intensity normalization + data.normalized <- data[,1]/bioFactor[1] + for (i in 2:ncol(data)) + data.normalized <- cbind(data.normalized,data[,i]/bioFactor[i]) + colnames(data.normalized) <- colnames(data) + rownames(data.normalized) <- rownames(data) + return(data.normalized) + } + + + ################################################################################################################# + # Probabilistic quotient normalization (PQN) + # Input parameters + # - data : bucketed spectra (rows=buckets; columns=samples) + # - sampleMetadata : dataframe with treatment group of inviduals + # - pqnFactor : number of the column cotaining the biological facor of interest + # - nomControl : name of the treatment group + ################################################################################################################# + NmrBrucker_pqn <- function(data,sampleMetadata,pqnFactor,nomControl) + { + # Total intensity normalization + data.total <- apply(data,2,sum) + data.normalized <- data[,1]/data.total[1] + for (i in 2:ncol(data)) + data.normalized <- cbind(data.normalized,data[,i]/data.total[i]) + colnames(data.normalized) <- colnames(data) + rownames(data.normalized) <- rownames(data) + + # Reference spectrum + # Recuperation spectres individus controle + control.spectra <- data.normalized[,sampleMetadata[,pqnFactor]==nomControl] + spectrum.ref <- apply(control.spectra,1,median) + + # 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) + + # Normalization + data.normalizedPQN <- data.normalized[,1]/data.normalized.ref.median + for (i in 2:ncol(data)) + data.normalizedPQN <- cbind(data.normalizedPQN,data.normalized[,i]/data.normalized.ref.median) + colnames(data.normalizedPQN) <- colnames(data) + rownames(data.normalizedPQN) <- rownames(data) + + return(data.normalizedPQN) + } + + + ## Tests + if (scalingMethod=="QuantitativeVariable") + { + if(mode(sampleMetadata[,bioFactor]) == "character") + bioFact <- factor(sampleMetadata[,bioFactor]) + else + bioFact <- sampleMetadata[,bioFactor] + } + + ## Spectra scaling depending on the user choice + if (scalingMethod == "None") + { + NormalizedBucketedSpectra <- dataMatrix + } + else if (scalingMethod == "Total") + { + NormalizedBucketedSpectra <- NmrBrucker_total(dataMatrix) + } + else if (scalingMethod == "PQN") + { + NormalizedBucketedSpectra <- NmrBrucker_pqn(dataMatrix,sampleMetadata,bioFactor,ControlGroup) + } + else if (scalingMethod == "QuantitativeVariable") + { + NormalizedBucketedSpectra <- NmrBrucker_bioFact(dataMatrix,sampleMetadata,bioFact) + } + + ## OUTPUTS + return(list(NormalizedBucketedSpectra)) + +} |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/NmrNormalization_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/NmrNormalization_wrapper.R Thu Mar 02 10:27:05 2017 -0500 |
| [ |
| @@ -0,0 +1,139 @@ +#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file + +## 070115_NmrBucketing2galaxy_v1.R +## Marie Tremblay-Franco +## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics +## www.metabohub.fr/en +## marie.tremblay-franco@toulouse.inra.fr + +runExampleL <- FALSE + + +##------------------------------ +## Options +##------------------------------ +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + + +##------------------------------ +## Libraries laoding +##------------------------------ +# For parseCommandArgs function +library(batch) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} +#Import the different functions +source_local("NmrNormalization_script.R") +source_local("DrawSpec.R") + + +##------------------------------ +## Errors ????????????????????? +##------------------------------ + + +##------------------------------ +## Constants +##------------------------------ +topEnvC <- environment() +flagC <- "\n" + + +##------------------------------ +## Script +##------------------------------ +if(!runExampleL) + argLs <- parseCommandArgs(evaluate=FALSE) + + +## Parameters Loading +##------------------- + # Inputs +data <- read.table(argLs[["dataMatrix"]],check.names=FALSE,header=TRUE,sep="\t") +rownames(data) <- data[,1] +data <- data[,-1] + +scaling <- argLs[["scalingMethod"]] +graphique <- argLs[["graphType"]] + +if (scaling=='PQN') +{ + metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t") + factor<- argLs[["factor"]] + ControlGroup <- argLs[["controlGroup"]] +} +if (scaling=='QuantitativeVariable') +{ + metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t") + factor <- argLs[["factor"]] +} + + # Outputs +nomGraphe <- argLs[["graphOut"]] +dataMatrixOut <- argLs[["dataMatrixOut"]] +log <- argLs[["logOut"]] + +## Checking arguments +##------------------- +error.stock <- "\n" + +if(length(error.stock) > 1) + stop(error.stock) + + +## Computation +##------------ +NormalizationResults <- NmrNormalization(dataMatrix=data,scalingMethod=scaling,sampleMetadata=metadataSample, + bioFactor=factor,ControlGroup=ControlGroup, + graph=graphique,nomFichier=nomGraphe,savLog.txtC=log) + +data_normalized <- NormalizationResults[[1]] + + +## Graphical outputs +##------------------ +if (graphique != "None") +{ + # Graphic Device opening + pdf(nomGraphe,onefile=TRUE) + + if (graphique == "Overlay") + { + # Global spectral window + spectra <- data.frame(t(data_normalized)) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + } + else + { + for (i in 1:ncol(data_normalized)) + { + spectra <- t(data_normalized[,i]) + drawSpec(spectra,xlab="", ylab="Intensity", main=colnames(data_normalized)[i]) + } + } + dev.off() +} + + +## Saving +##------- + # Data +data_normalized <- cbind(rownames(data_normalized),data_normalized) +colnames(data_normalized) <- c("Bucket",colnames(data_normalized)[-1]) +write.table(data_normalized,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t") + + +## Ending +##--------------------- +cat("\nEnd of 'Normalization' Galaxy module call: ", as.character(Sys.time()), sep = "") + +options(stringsAsFactors = strAsFacL) + +rm(list = ls()) |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/NmrNormalization_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/NmrNormalization_xml.xml Thu Mar 02 10:27:05 2017 -0500 |
| b |
| b'@@ -0,0 +1,260 @@\n+<tool id="normalization" name="Normalization" version="2.0.1">\r\n+\r\n+ <description> Normalization of (preprocessed) spectra </description>\r\n+\r\n+ <requirements>\r\n+ <requirement type="package" version="1.1_4">r-batch</requirement>\r\n+ </requirements>\r\n+\r\n+ <stdio>\r\n+ <exit_code range="1:" level="fatal" />\r\n+ </stdio>\r\n+\r\n+ <command>\r\n+ Rscript $__tool_directory__/NmrNormalization_wrapper.R\r\n+\r\n+ ## Data matrix of bucketed and integrated spectra\r\n+ dataMatrix $dataMatrix\r\n+\r\n+ ## Normalization method\r\n+ scalingMethod $scalingMethod.method\r\n+ #if $scalingMethod.method == "PQN":\r\n+ ## Sample metadata matrix\r\n+ sampleMetadata $scalingMethod.sampleMetadata\r\n+\r\n+ ## Biological factor of interest (column number in samplemetadata)\r\n+ factor $scalingMethod.factor\r\n+\r\n+ ## Reference class\r\n+ controlGroup $scalingMethod.controlGroup\r\n+ #end if\r\n+ #if $scalingMethod.method == "QuantitativeVariable":\r\n+ ## Sample metadata matrix\r\n+ sampleMetadata $scalingMethod.sampleMetadata\r\n+\r\n+ ## Biological factor of interest (column number in samplemetadata)\r\n+ factor $scalingMethod.factor\r\n+ #end if\r\n+\r\n+ ## Spectra representation\r\n+ graphType $graphType\r\n+\r\n+ ## Outputs\r\n+ logOut $logOut\r\n+ dataMatrixOut $dataMatrixOut\r\n+ graphOut $graphOut\r\n+\r\n+\r\n+ </command>\r\n+\r\n+ <inputs>\r\n+ <param name="dataMatrix" type="data" label="Data matrix of preprocessed data" help="" format="tabular" />\r\n+\r\n+ <conditional name="scalingMethod" >\r\n+ <param name="method" label="Normalization method" type="select" help="Default method is total intensity" >\r\n+ <option value="None">None normalization</option>\r\n+ <option value="Total">Total intensity</option>\r\n+ <option value="PQN">Probabilistic Quotient Normalization</option>\r\n+ <option value="QuantitativeVariable">Quantitative variable</option>\r\n+ </param>\r\n+ <when value="None" />\r\n+ <when value="Total" />\r\n+ <when value="PQN">\r\n+ <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />\r\n+ <param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" />\r\n+ <param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/>\r\n+ </when>\r\n+ <when value="QuantitativeVariable">\r\n+ <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />\r\n+ <param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" />\r\n+ </when>\r\n+ </conditional>\r\n+\r\n+ <param name="graphType" label="Spectra representation" type="select" help="Select \'None\' for no representation,\'Overlay\' to overlay all spectra on a unique chart and \'One per individual\' to generate an individual chart for each observation">\r\n+ <option value="None"> none </option>\r\n+ <option value="Overlay"> Overlay </option>\r\n+ <option value="One_per_individual"> One_per_individual </option>\r\n+ </param>\r\n+ </inputs>\r\n+\r\n+\r\n+ <outputs>\r\n+ <data format="txt" name="logOut" label="${tool.name}_log" />\r\n+ <data format="tabular" name="dataMatrixOut" label="${tool.name}_dataMatrix" />\r\n+ <data format="pdf" name="graphOut" label="${tool.name}_spectra" >\r\n+ <filter> graphType != "None" </filter>\r\n+ </data>\r\n+ </outputs>\r\n+\r\n+ <tests>\r\n+ <test>\r\n+ <param na'..b' | parameter |\r\n++======================+====================================+=========+=============+\r\n+| NMR_Bucketing | Normalization_bucketedData.tsv | tabular | Ions Matrix |\r\n++----------------------+------------------------------------+---------+-------------+\r\n+\r\n+\r\n+\r\n+\r\n+**Downstream tools**\r\n+\r\n++---------------------------+----------------------+--------+\r\n+| Name | Output file | Format |\r\n++===========================+======================+========+\r\n+|Univariate | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+|Multivariate | sampleMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+| | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+\r\n+\r\n+-----------\r\n+Input files\r\n+-----------\r\n+\r\n++---------------------------+------------+\r\n+| Parameter : num + label | Format |\r\n++===========================+============+\r\n+| DataMatrix | Tabular |\r\n++---------------------------+------------+\r\n+\r\n+**DataMAtrix**\r\n+\r\n+ | variable x sample dataMatrix tabular separated file containing (preprocessed) spectra, with . as decimal, and NA for missing values\r\n+\r\n+\r\n+----------\r\n+Parameters\r\n+----------\r\n+\r\n+DataMatrix\r\n+ | see "Input files" section above\r\n+ |\r\n+\r\n+Normalization method\r\n+ | normalization to apply on each spectrum:\r\n+\r\n++---------------------------+--------------------------------------+\r\n+| Name | Normalization |\r\n++===========================+======================================+\r\n+|None | No |\r\n++---------------------------+--------------------------------------+\r\n+|Total | Total intensity |\r\n++---------------------------+--------------------------------------+\r\n+|PQN | Probabilistic Quotient Normalization |\r\n++---------------------------+--------------------------------------+\r\n+|QuantitativeVariable | Weight, osmolality, ... |\r\n++---------------------------+--------------------------------------+\r\n+\r\n+\r\n+sampleMetadata\r\n+ | sample x metadata **sample** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values\r\n+ | Mandatory for "PQN" or "Quantitative" normalization method\r\n+ | The row names must be identical to the column names of the dataMatrix file\r\n+ |\r\n+\r\n+\r\n+Spectra representation:\r\n+ | Graphical chart of bucketed and integrated raw files\r\n+ | If "Overlay": the n (sample number) spectra are overlaid on the same figure\r\n+ | If "One_per_individual": pdf file includes n pages (1 per sample)\r\n+ |\r\n+\r\n+\r\n+------------\r\n+Output files\r\n+------------\r\n+\r\n+\r\n+dataMatrix.tsv\r\n+ | tabular output\r\n+ | Data matrix with p rows (variable) and n columns (samples) containing the intensities\r\n+ |\r\n+\r\n+spectra.pdf\r\n+ | pdf output\r\n+ | Graphical chart of bucketed and integrated data\r\n+ |\r\n+\r\n+\r\n+---------------------------------------------------\r\n+\r\n+---------------\r\n+Working example\r\n+---------------\r\n+\r\n+\r\n+.. class:: warningmark\r\n+\r\n+Under construction\r\n+\r\n+.. image:: ./static/images/Mth_Travaux.png\r\n+ :width: 100\r\n+\r\n+\r\n+---------------------------------------------------\r\n+\r\n+--------------\r\n+Changelog/News\r\n+--------------\r\n+\r\n+**Version 1.0.2 - 22/10/2016**\r\n+\r\n+- NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data\r\n+\r\n+**Version 1.0.1 - 14/04/2016**\r\n+\r\n+- TEST: refactoring to pass planemo test using conda dependencies\r\n+\r\n+**Version 2015-01-28 - 28/01/2015**\r\n+\r\n+ </help>\r\n+ <citations>\r\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\r\n+ </citations>\r\n+</tool>\r\n' |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/README.rst Thu Mar 02 10:27:05 2017 -0500 |
| b |
| @@ -0,0 +1,22 @@ + +Changelog/News +-------------- + +**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 + +**Version 1.0.1 - 14/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + +**Version 2015-01-28 - 28/01/2015** + + + +Test Status +----------- + +Planemo test using conda: passed + +Planemo shed_test: passed |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/planemo_test.sh Thu Mar 02 10:27:05 2017 -0500 |
| [ |
| @@ -0,0 +1,12 @@ +planemo conda_init +planemo conda_install . +planemo test --install_galaxy --conda_dependency_resolution + +#All 1 test(s) executed passed. +#NmrNormalization[0]: passed + +planemo shed_test --install_galaxy -t testtoolshed + +#All 1 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/nmr_normalization/NmrNormalization/1.0.1[0]: passed + |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/test-data/MTBLS1_bucketedData.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/test-data/MTBLS1_bucketedData.tabular Thu Mar 02 10:27:05 2017 -0500 |
| b |
| b'@@ -0,0 +1,595 @@\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\r\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\r\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\r\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\r\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\r\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\r\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\r\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\r\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\t1.488989398'..b'2263392642444\t0.00538943800528357\t0.00514775819006039\t0.00559553789396426\t0.0173520429506117\t0.028324033261543\r\n+B0.876\t0.00215863677466562\t0.00369895246404019\t0.00360045348807487\t0.00134769212206423\t0.00218354336599731\t0.00245532683379321\t0.00345022433982449\t0.000717888096909645\t0.00170401747506495\t0.000356847987108017\t0.0041628951177036\t0.005088145578844\t0.00284987245949532\t0.00268286392210182\t0.00197915272339639\t0.0164744229799929\t0.00871859567919084\t0.0291624658349522\t0.00450433606743076\t0.00467317787458834\t0.00464469278467577\t0.0176322957897126\t0.0298903125539951\r\n+B0.866\t0.00150013418482023\t0.00258508360037412\t0.00238111738536749\t0.000983712268869988\t0.00157378746779101\t0.00184741600638927\t0.00259613706860757\t0.000530590445564721\t0.00114218607490948\t0.000297719443003154\t0.00236377135640083\t0.00299039447289031\t0.00169838032153178\t0.00202478720109677\t0.00155237208983581\t0.00506508824735588\t0.00335278099612616\t0.00916049409218431\t0.00304824370929634\t0.0028945285734165\t0.0028543532645478\t0.00397438831823791\t0.00746021084696681\r\n+B0.857\t0.000986962374512856\t0.00174301185204418\t0.00155459274530862\t0.00059744100374567\t0.000946611593982685\t0.00119641009019251\t0.00173321235334005\t0.000356899004924163\t0.000758730491964375\t0.000160811437925477\t0.00152510957100737\t0.00196835887814581\t0.00101457930295155\t0.00150335976451684\t0.00101420955937978\t0.0033735623219071\t0.00210956426055451\t0.00493276854725743\t0.00178283936255044\t0.00165275426730159\t0.00170372495712446\t0.00248870525573775\t0.0039846322834038\r\n+B0.846\t0.000839825601114667\t0.0012769784113784\t0.00110091918664795\t0.000413961172391942\t0.000708888771217311\t0.000778154520699405\t0.00111234240481985\t0.000244663266226838\t0.000484525523691875\t7.68758960306947e-05\t0.000909219126236251\t0.00113056799032888\t0.000631562997579227\t0.00107030332221529\t0.000634580995745331\t0.00106135884542878\t0.000970558123349218\t0.00157698752726719\t0.00109118524592164\t0.0010809000005087\t0.00117405624971632\t0.00104182637112804\t0.00136932315987551\r\n+B0.836\t0.000540291147081289\t0.00110805916107828\t0.000991944918364915\t0.000259305489167024\t0.000414200683547401\t0.000446851710747917\t0.000739324952553648\t0.00014512091218808\t0.000240131270356258\t1.53279187890163e-05\t0.000995779500719967\t0.00117589795062701\t0.000663607401633198\t0.00072607607121414\t0.000348533637762843\t0.000814771690737036\t0.000852228105038011\t0.00106417265964175\t0.00106436355116083\t0.00088998568772594\t0.00115577335390134\t0.000793475313473202\t0.000969704476916626\r\n+B0.826\t0.000439210376659004\t0.000622025753244184\t0.0005877341421479\t0.000201776175879904\t0.000325527630159852\t0.000344597178120722\t0.000468730496980652\t0.000169188243600758\t0.000244354283493434\t1.80591932027473e-05\t0.000645393534597378\t0.00076364124043746\t0.000411619698520102\t0.000416731585656504\t0.000256480294202034\t0.000524752271786902\t0.000676304092825243\t0.000814916554483356\t0.000597779964300897\t0.000807012376046873\t0.000712066733726576\t0.000508127245813254\t0.000691958647587166\r\n+B0.816\t0.000394076959769821\t0.000626251816952311\t0.000644546372165628\t0.000163741793970591\t0.000294493619073591\t0.000396363737760121\t0.000520046367222883\t0.00012853568638618\t0.000243131055493038\t1.18743008584546e-05\t0.000604929046893319\t0.000717510278393041\t0.000373029125568352\t0.000391937364448496\t0.000234261393789731\t0.000523235700797077\t0.000619868853421147\t0.000730622691788109\t0.000640770168804395\t0.000676985988978989\t0.000745527871203007\t0.00061791716531139\t0.000781012740687151\r\n+B0.806\t0.000336785447055572\t0.000470318285990568\t0.000447571911175899\t0.00015477142985862\t0.000254766661248894\t0.000300355488014835\t0.000386815449880438\t0.000128859420585409\t0.000182934749398549\t1.11417886043334e-05\t0.0003939533156056\t0.000417332638774188\t0.000210616293653824\t0.000296880999894829\t0.000120837576055159\t0.00033047173709954\t0.000388172417071423\t0.000450376987152908\t0.000452051328977898\t0.000485123182275246\t0.00047918667429437\t0.000397128925502763\t0.000516124725384787\r\n+B0.8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n' |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/test-data/MTBLS1_bucketedData_normalized.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/test-data/MTBLS1_bucketedData_normalized.tabular Thu Mar 02 10:27:05 2017 -0500 |
| b |
| b'@@ -0,0 +1,595 @@\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\r\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\r\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\r\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\r\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\r\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\r\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\r\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\r\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\t8.00'..b'6\t0.00205900121174115\t0.00222772007237317\t0.00655696126430037\t0.0090775419089283\r\n+B0.876\t0.00153795992686315\t0.00163175750076373\t0.00197325573544149\t0.00166007906880872\t0.00192850855060131\t0.00198972441486426\t0.00200424498414009\t0.00172801308114746\t0.00157954222895385\t0.00174137194096089\t0.00223908076509186\t0.00253113263350169\t0.00160724207847848\t0.00157803156538568\t0.00204432750279849\t0.00630622549828998\t0.00325770211049173\t0.00897169131164893\t0.0017178213156727\t0.00186917849502687\t0.00184916544977564\t0.0066628627431882\t0.00957951723804306\r\n+B0.866\t0.00106879781177101\t0.00114038490519135\t0.00130498937231046\t0.00121173086979251\t0.00138997128966015\t0.0014970914184345\t0.00150810329572991\t0.00127717291123033\t0.00105875154747096\t0.00145283230690403\t0.00127139282339446\t0.00148759207457571\t0.000957835256427262\t0.00119095794989723\t0.00160349270691048\t0.00193885932729513\t0.00125276617118119\t0.00281818162162267\t0.00116251051005198\t0.00115775403972774\t0.00113638763271284\t0.00150183527819445\t0.00239091572826001\r\n+B0.857\t0.000703179246799224\t0.000768913007437415\t0.00085200629896102\t0.000735924243325799\t0.000836048681936822\t0.000969535433687392\t0.00100682791131435\t0.000859083960038255\t0.000703306667912533\t0.000784738981039103\t0.000820304958099411\t0.000979173514931066\t0.000572192114150215\t0.000884259966744718\t0.00104760813621454\t0.00129136205621995\t0.000788238404061898\t0.00151754234255332\t0.000679922504351758\t0.000661068937864078\t0.000678294447596055\t0.00094042782204835\t0.00127703093024458\r\n+B0.846\t0.000598348983593219\t0.000563326812479259\t0.000603367077648935\t0.000509914888079037\t0.000626091552843253\t0.000630593461963119\t0.000646162818971916\t0.000588923714345205\t0.000449131852740021\t0.000375144411963733\t0.000489038277268019\t0.000562408738187872\t0.000356182474600669\t0.000629540847405227\t0.000655478158415776\t0.00040627633647667\t0.000362648913096872\t0.000485152571700731\t0.000416145963962437\t0.000432338569266074\t0.000467420420190424\t0.000393683624404144\t0.000438853049488296\r\n+B0.836\t0.000384940228389589\t0.000488809700842862\t0.000543642906619575\t0.000319410945531124\t0.000365822622222678\t0.000362115440788554\t0.000429475936014247\t0.000349317443329355\t0.000222590136292813\t7.47982576806319e-05\t0.000535596180853289\t0.0005849584353237\t0.000374254551617207\t0.000427070098415394\t0.000360011075904364\t0.000311885522039264\t0.000318434917566949\t0.000327387562445399\t0.000405916958334785\t0.000355976629399232\t0.000460141553572065\t0.00029983713787655\t0.000310779645935444\r\n+B0.826\t0.000312923399940064\t0.000274400711658721\t0.000322112136915352\t0.0002485466826425\t0.000287506457621244\t0.000279251384851633\t0.000272286858753872\t0.0004072494019291\t0.000226504666326223\t8.81265229335221e-05\t0.00034713539697075\t0.000379878530204733\t0.000232141090239979\t0.000245117015082896\t0.000264926356195127\t0.00020086932092535\t0.000252700933911809\t0.000250705129427516\t0.000227975699278555\t0.000322788949834321\t0.000283491129119682\t0.000192010282455859\t0.000221765154867484\r\n+B0.816\t0.000280767278376387\t0.000276264999243242\t0.000353248508791008\t0.000201696159241044\t0.000260097175684691\t0.000321201477267197\t0.000302096391529068\t0.000309395501089554\t0.000225370792812284\t5.79450496583063e-05\t0.000325370914915426\t0.000356930369300896\t0.000210377171481443\t0.000230533322118424\t0.000241975773019886\t0.000200288794453642\t0.000231613914249728\t0.000224772531002939\t0.000244370899049553\t0.000270780973032295\t0.000296812823836662\t0.000233497515481325\t0.000250306014667077\r\n+B0.806\t0.000239948900899456\t0.000207476413490648\t0.00024529516731032\t0.000190646518556741\t0.000225010271047323\t0.00024339922466384\t0.0002247021784242\t0.000310174754755259\t0.00016957171275904\t5.43704847684375e-05\t0.000211894190551516\t0.000207604960325587\t0.000118781234734116\t0.000174622195757986\t0.000124816835598791\t0.000126500897633393\t0.000145040571768504\t0.0001385562978616\t0.000172399083254758\t0.000194039654402791\t0.000190775899112539\t0.000150066420931897\t0.000165412311927898\r\n+B0.8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n' |
| b |
| diff -r 000000000000 -r 6361c0753d03 normalization/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/tool_dependencies.xml Thu Mar 02 10:27:05 2017 -0500 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="r-batch" version="1.1_4"> + <repository changeset_revision="e8a964ca8656" name="package_r_batch_1_1_4" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |