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normalization/.travis.yml normalization/README.md normalization/galaxy/normalization/.shed.yml normalization/galaxy/normalization/DrawSpec.R normalization/galaxy/normalization/MANUAL_INSTALL.txt normalization/galaxy/normalization/NmrNormalization_script.R normalization/galaxy/normalization/NmrNormalization_wrapper.R normalization/galaxy/normalization/NmrNormalization_xml.xml normalization/galaxy/normalization/README.rst normalization/galaxy/normalization/planemo_test.sh normalization/galaxy/normalization/test-data/MTBLS1_bucketedData.tabular normalization/galaxy/normalization/test-data/MTBLS1_bucketedData_normalized.tabular normalization/galaxy/normalization/tool_dependencies.xml |
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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 |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/.shed.yml --- a/normalization/.shed.yml Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -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 |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/.travis.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/.travis.yml Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -0,0 +1,16 @@ + +# This is a special configuration file to run tests on Travis-CI via +# GitHub notifications when changes are committed. +# +# See http://travis-ci.org/ for details +language: python + +before_install: + - export GALAXY_RELEASE=release_17.01 + - export PLANEMO_RELEASE=0.37.0 + +install: + - pip install planemo==$PLANEMO_RELEASE + +script: + - planemo lint ${TRAVIS_BUILD_DIR}/galaxy/normalization && planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch $GALAXY_RELEASE --no_cache_galaxy ${TRAVIS_BUILD_DIR}/galaxy/normalization |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/DrawSpec.R --- a/normalization/DrawSpec.R Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,74 +0,0 @@ -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 |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/MANUAL_INSTALL.txt --- a/normalization/MANUAL_INSTALL.txt Thu Mar 02 10:27:05 2017 -0500 +++ /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 6361c0753d03 -r f9554d5bb47e normalization/NmrNormalization_script.R --- a/normalization/NmrNormalization_script.R Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,147 +0,0 @@ -################################################################################################################# -# 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)) - -} |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/NmrNormalization_wrapper.R --- a/normalization/NmrNormalization_wrapper.R Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,139 +0,0 @@ -#!/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()) |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/NmrNormalization_xml.xml --- a/normalization/NmrNormalization_xml.xml Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,260 +0,0 @@\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' |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/README.md Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -0,0 +1,73 @@ +Spectral Normalization for Galaxy +================================= + +[](http://bioconda.github.io) [](https://travis-ci.org/workflow4metabolomics/normalization) + +Our project +----------- +The [Workflow4Metabolomics](http://workflow4metabolomics.org), W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform. + + +Normalization +------------- + +Normalization (operation applied on each individual spectrum) of preprocessed data + + +Galaxy +------ +Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. + +Homepage: [https://galaxyproject.org/](https://galaxyproject.org/) + + +Dependencies using Conda +------------------------ +[](http://bioconda.github.io) + +[Conda](http://conda.pydata.org/) is package manager that among many other things can be used to manage Python packages. + +``` +#To install miniconda2 +#http://conda.pydata.org/miniconda.html +#To install the R library using conda: +conda install r-batch +#To set an environment: +conda create -n r-batch r-batch` +#To activate the environment: +. activate r-batch +``` + +Test Status +----------- + +Planemo test using conda: passed + +Planemo shed_test: passed + + +Conda +----- +[](http://bioconda.github.io) + +[Conda](http://conda.pydata.org/) is package manager that among many other things can be used to manage Python packages. + +Travis +------ +[](https://travis-ci.org/workflow4metabolomics/spectral_normalization) + +Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes! + +Test Status +----------- + +Planemo test using conda: passed + +Planemo shed_test: passed + + +Historic contributors +--------------------- + - Marie Tremblay-Franco @mtremblayfr - [French Metabolomics and Fluxomics Infrastructure (MetaboHUB)](http://www.metabohub.fr/en) - [MetaToul](http://www.metatoul.fr/) + - Marion Landi - [French Metabolomics and Fluxomics Infrastructure (MetaboHUB)](http://www.metabohub.fr/en) - [La plateforme "Exploration du Métabolisme" (PFEM, Clermont-Ferrand)](http://www6.clermont.inra.fr/plateforme_exploration_metabolisme) + - Gildas Le Corguillé @lecorguille - [ABiMS](http://abims.sb-roscoff.fr/) / [IFB](http://www.france-bioinformatique.fr/) - [UPMC](www.upmc.fr)/[CNRS](www.cnrs.fr) - [Station Biologique de Roscoff](http://www.sb-roscoff.fr/) - France |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/README.rst --- a/normalization/README.rst Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ - -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 |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/.shed.yml Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -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 |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/DrawSpec.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/DrawSpec.R Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -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 |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/MANUAL_INSTALL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/MANUAL_INSTALL.txt Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -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/$library + + + +Finally, restart Galaxy |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/NmrNormalization_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/NmrNormalization_script.R Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -0,0 +1,147 @@ +################################################################################################################# +# SPECTRA NORMALIZATION FROM SPECTRAL DATA # +# User : Galaxy # +# Original data : -- # +# Starting date : 20-10-2014 # +# Version 1 : 27-01-2015 # +# Version 2 : 27-02-2015 # +# # +# Input files: # +# - Data matrix containing bucketed and integrated spectra to normalize # +# - Sample metadata matrix containing at least biological factor of interest # +# - Scaling method: Total intensity/Probabilistic Quotient Normalization # +# - Control group: name of control to compute median reference spectra # +# - Graph: normalization result representation # +################################################################################################################# +NmrNormalization <- function(dataMatrix,scalingMethod=c("None","Total","PQN","BioFactor"),sampleMetadata=NULL, + bioFactor=NULL,ControlGroup=NULL,graph=c("None","Overlay","One_per_individual"), + nomFichier=NULL,savLog.txtC=NULL) +{ + + ## Option + ##--------------- + strAsFacL <- options()$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)) + +} |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/NmrNormalization_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/NmrNormalization_wrapper.R Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -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()) |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/NmrNormalization_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/NmrNormalization_xml.xml Thu Mar 02 12:23:13 2017 -0500 |
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| b'@@ -0,0 +1,261 @@\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="3.1.2">R</requirement>\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+ '..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' |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/README.rst Thu Mar 02 12:23:13 2017 -0500 |
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| @@ -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 |
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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/planemo_test.sh Thu Mar 02 12:23:13 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 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/test-data/MTBLS1_bucketedData.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/test-data/MTBLS1_bucketedData.tabular Thu Mar 02 12:23:13 2017 -0500 |
| b |
| b'@@ -0,0 +1,595 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|
| b |
| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/test-data/MTBLS1_bucketedData_normalized.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/test-data/MTBLS1_bucketedData_normalized.tabular Thu Mar 02 12:23:13 2017 -0500 |
| b |
| b'@@ -0,0 +1,595 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|
| b |
| diff -r 6361c0753d03 -r f9554d5bb47e normalization/galaxy/normalization/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalization/galaxy/normalization/tool_dependencies.xml Thu Mar 02 12:23:13 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> |
| b |
| diff -r 6361c0753d03 -r f9554d5bb47e normalization/planemo_test.sh --- a/normalization/planemo_test.sh Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,12 +0,0 @@ -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 6361c0753d03 -r f9554d5bb47e normalization/test-data/MTBLS1_bucketedData.tabular --- a/normalization/test-data/MTBLS1_bucketedData.tabular Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,595 +0,0 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| diff -r 6361c0753d03 -r f9554d5bb47e normalization/test-data/MTBLS1_bucketedData_normalized.tabular --- a/normalization/test-data/MTBLS1_bucketedData_normalized.tabular Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r 6361c0753d03 -r f9554d5bb47e normalization/tool_dependencies.xml --- a/normalization/tool_dependencies.xml Thu Mar 02 10:27:05 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?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> |