| Previous changeset 2:3cd762aac7a4 (2017-04-20) Next changeset 4:8178d9a118e3 (2018-01-30) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990 |
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added:
DrawSpec.R MANUAL_INSTALL.txt NmrNormalization_script.R NmrNormalization_wrapper.R NmrNormalization_xml.xml README.rst planemo_test.sh test-data/MTBLS1_bucketedData.tabular test-data/MTBLS1_bucketedData_normalized.tabular |
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removed:
nmr_bucketing/.shed.yml nmr_bucketing/DrawSpec.R nmr_bucketing/MANUAL_INSTALL.txt nmr_bucketing/NmrBucketing_script.R nmr_bucketing/NmrBucketing_wrapper.R nmr_bucketing/NmrBucketing_xml.xml nmr_bucketing/README.rst nmr_bucketing/planemo_test.sh nmr_bucketing/repository_dependencies.xml nmr_bucketing/static/images/MTH - Architecture repertoire Bruker.png nmr_bucketing/static/images/Mth_Travaux.png nmr_bucketing/test-data/MTBLS1.zip nmr_bucketing/test-data/MTBLS1_bucketedData.tabular nmr_bucketing/test-data/MTBLS1_sampleMetadata.tabular nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e DrawSpec.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DrawSpec.R Thu Oct 26 06:01:14 2017 -0400 |
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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 3cd762aac7a4 -r 966fcf7ae66e MANUAL_INSTALL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MANUAL_INSTALL.txt Thu Oct 26 06:01:14 2017 -0400 |
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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/$library + + + +Finally, restart Galaxy |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e NmrNormalization_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrNormalization_script.R Thu Oct 26 06:01:14 2017 -0400 |
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| @@ -0,0 +1,147 @@ +################################################################################################################# +# SPECTRA NORMALIZATION FROM SPECTRAL DATA # +# User : Galaxy # +# Original data : -- # +# Starting date : 20-10-2014 # +# Version 1 : 27-01-2015 # +# Version 2 : 27-02-2015 # +# # +# Input files: # +# - Data matrix containing bucketed and integrated spectra to normalize # +# - Sample metadata matrix containing at least biological factor of interest # +# - Scaling method: Total intensity/Probabilistic Quotient Normalization # +# - Control group: name of control to compute median reference spectra # +# - Graph: normalization result representation # +################################################################################################################# +NmrNormalization <- function(dataMatrix,scalingMethod=c("None","Total","PQN","BioFactor"),sampleMetadata=NULL, + bioFactor=NULL,ControlGroup=NULL,graph=c("None","Overlay","One_per_individual"), + nomFichier=NULL,savLog.txtC=NULL) +{ + + ## Option + ##--------------- + strAsFacL <- options()$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 3cd762aac7a4 -r 966fcf7ae66e NmrNormalization_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrNormalization_wrapper.R Thu Oct 26 06:01:14 2017 -0400 |
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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 3cd762aac7a4 -r 966fcf7ae66e NmrNormalization_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrNormalization_xml.xml Thu Oct 26 06:01:14 2017 -0400 |
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| b'@@ -0,0 +1,260 @@\n+<tool id="normalization" name="Normalization" version="1.0.2">\n+\n+ <description> Normalization of (preprocessed) spectra </description>\n+\n+ <requirements>\n+ <requirement type="package" version="1.1_4">r-batch</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+\n+ <command>\n+ Rscript $__tool_directory__/NmrNormalization_wrapper.R\n+\n+ ## Data matrix of bucketed and integrated spectra\n+ dataMatrix $dataMatrix\n+\n+ ## Normalization method\n+ scalingMethod $scalingMethod.method\n+ #if $scalingMethod.method == "PQN":\n+ ## Sample metadata matrix\n+ sampleMetadata $scalingMethod.sampleMetadata\n+\n+ ## Biological factor of interest (column number in samplemetadata)\n+ factor $scalingMethod.factor\n+\n+ ## Reference class\n+ controlGroup $scalingMethod.controlGroup\n+ #end if\n+ #if $scalingMethod.method == "QuantitativeVariable":\n+ ## Sample metadata matrix\n+ sampleMetadata $scalingMethod.sampleMetadata\n+\n+ ## Biological factor of interest (column number in samplemetadata)\n+ factor $scalingMethod.factor\n+ #end if\n+\n+ ## Spectra representation\n+ graphType $graphType\n+\n+ ## Outputs\n+ logOut $logOut\n+ dataMatrixOut $dataMatrixOut\n+ graphOut $graphOut\n+\n+\n+ </command>\n+\n+ <inputs>\n+ <param name="dataMatrix" type="data" label="Data matrix of preprocessed data" help="" format="tabular" />\n+\n+ <conditional name="scalingMethod" >\n+ <param name="method" label="Normalization method" type="select" help="Default method is total intensity" >\n+ <option value="None">None normalization</option>\n+ <option value="Total">Total intensity</option>\n+ <option value="PQN">Probabilistic Quotient Normalization</option>\n+ <option value="QuantitativeVariable">Quantitative variable</option>\n+ </param>\n+ <when value="None" />\n+ <when value="Total" />\n+ <when value="PQN">\n+ <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />\n+ <param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" />\n+ <param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/>\n+ </when>\n+ <when value="QuantitativeVariable">\n+ <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />\n+ <param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" />\n+ </when>\n+ </conditional>\n+\n+ <param name="graphType" label="Spectra representation" type="select" help="Select \'None\' for no representation,\'Overlay\' to overlay all spectra on a unique chart and \'One per individual\' to generate an individual chart for each observation">\n+ <option value="None"> none </option>\n+ <option value="Overlay"> Overlay </option>\n+ <option value="One_per_individual"> One_per_individual </option>\n+ </param>\n+ </inputs>\n+\n+\n+ <outputs>\n+ <data format="txt" name="logOut" label="${tool.name}_log" />\n+ <data format="tabular" name="dataMatrixOut" label="${tool.name}_dataMatrix" />\n+ <data format="pdf" name="graphOut" label="${tool.name}_spectra" >\n+ <filter> graphType != "None" </filter>\n+ </data>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" />\n+ <condi'..b'-------------------------------+---------+-------------+\n+| Name | output file | format | parameter |\n++======================+====================================+=========+=============+\n+| NMR_Bucketing | Normalization_bucketedData.tsv | tabular | Ions Matrix |\n++----------------------+------------------------------------+---------+-------------+\n+\n+\n+\n+\n+**Downstream tools**\n+\n++---------------------------+----------------------+--------+\n+| Name | Output file | Format |\n++===========================+======================+========+\n+|Univariate | variableMetadata.tsv | Tabular|\n++---------------------------+----------------------+--------+\n+|Multivariate | sampleMetadata.tsv | Tabular|\n++---------------------------+----------------------+--------+\n+| | variableMetadata.tsv | Tabular|\n++---------------------------+----------------------+--------+\n+\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+------------+\n+| Parameter : num + label | Format |\n++===========================+============+\n+| DataMatrix | Tabular |\n++---------------------------+------------+\n+\n+**DataMAtrix**\n+\n+ | variable x sample dataMatrix tabular separated file containing (preprocessed) spectra, with . as decimal, and NA for missing values\n+\n+\n+----------\n+Parameters\n+----------\n+\n+DataMatrix\n+ | see "Input files" section above\n+ |\n+\n+Normalization method\n+ | normalization to apply on each spectrum:\n+\n++---------------------------+--------------------------------------+\n+| Name | Normalization |\n++===========================+======================================+\n+|None | No |\n++---------------------------+--------------------------------------+\n+|Total | Total intensity |\n++---------------------------+--------------------------------------+\n+|PQN | Probabilistic Quotient Normalization |\n++---------------------------+--------------------------------------+\n+|QuantitativeVariable | Weight, osmolality, ... |\n++---------------------------+--------------------------------------+\n+\n+\n+sampleMetadata\n+ | sample x metadata **sample** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values\n+ | Mandatory for "PQN" or "Quantitative" normalization method\n+ | The row names must be identical to the column names of the dataMatrix file\n+ |\n+\n+\n+Spectra representation:\n+ | Graphical chart of bucketed and integrated raw files\n+ | If "Overlay": the n (sample number) spectra are overlaid on the same figure\n+ | If "One_per_individual": pdf file includes n pages (1 per sample)\n+ |\n+\n+\n+------------\n+Output files\n+------------\n+\n+\n+dataMatrix.tsv\n+ | tabular output\n+ | Data matrix with p rows (variable) and n columns (samples) containing the intensities\n+ |\n+\n+spectra.pdf\n+ | pdf output\n+ | Graphical chart of bucketed and integrated data\n+ |\n+\n+\n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+\n+.. class:: warningmark\n+\n+Under construction\n+\n+.. image:: ./static/images/Mth_Travaux.png\n+ :width: 100\n+\n+\n+---------------------------------------------------\n+\n+--------------\n+Changelog/News\n+--------------\n+\n+**Version 1.0.2 - 22/10/2016**\n+\n+- NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data\n+\n+**Version 1.0.1 - 14/04/2016**\n+\n+- TEST: refactoring to pass planemo test using conda dependencies\n+\n+**Version 2015-01-28 - 28/01/2015**\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Oct 26 06:01:14 2017 -0400 |
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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 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/.shed.yml --- a/nmr_bucketing/.shed.yml Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -categories: [Metabolomics] -description: '[Metabolomics][W4M][NMR] NMR Bucketing - Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data' -homepage_url: http://workflow4metabolomics.org -long_description: 'Part of the W4M project: http://workflow4metabolomics.org' -name: nmr_bucketing -owner: marie-tremblay-metatoul -remote_repository_url: https://github.com/workflow4metabolomics/nmr_bucketing |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/DrawSpec.R --- a/nmr_bucketing/DrawSpec.R Thu Apr 20 08:53:46 2017 -0400 +++ /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 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/MANUAL_INSTALL.txt --- a/nmr_bucketing/MANUAL_INSTALL.txt Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,59 +0,0 @@ -Instructions to integrate the "NMR bucketing" tool into a local instance of Galaxy -Version February 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 and the "pracma" library, nessecary for cumtrapz 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/pracma_1.8.3.tar",lib="/usr/lib64/R/library",repos=NULL) - - - Finally, load the package into your R session -library(batch) -library(pracma) - - -## --- Config : --- ## - - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add -<section id="id_name" name="Name"> - <tool file="path/NmrBucketing_xml.xml" /> -</section> -to create a new section containing the NMR_Bucketing tool -or add - <tool file="path/NmrBucketing_xml.xml" /> -in an existing section - - - Put the three files NmrBucketing_xml.xml, NmrBucketing_wrapper.R and NmrBucketing_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/NmrBucketing_wrapper.R --args - - ## Library name for raw files storage - library path/$library - -## --- XML help part --- ## -one image: -Copy the 'Mth_Architecture_Repertoire_Bruker.png' file within the directory to your galaxy-dist/static/images/ - - - - Activate the "user_library_import_dir" in your /galaxy/dist/galaxy-dist/universe_wsgi.ini and create the users directories in this path, for example: - - #In universe_wsgi.ini - user_library_import_dir = /projet/sbr/galaxy/import/user - - #Create the user "myaccount" in this path - - User path: /projet/sbr/galaxy/import/user/myaccount@sb-roscoff.fr - - - - -Finally, restart Galaxy \ No newline at end of file |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/NmrBucketing_script.R --- a/nmr_bucketing/NmrBucketing_script.R Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,273 +0,0 @@\n-################################################################################################\r\n-# SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES #\r\n-# User : Galaxy #\r\n-# Original data : -- #\r\n-# Starting date : 20-10-2014 #\r\n-# Version 1 : 18-12-2014 #\r\n-# Version 2 : 07-01-2015 #\r\n-# Version 3 : 24-10-2016 #\r\n-# #\r\n-# Input files : modification on october 2016 #\r\n-# - Raw bruker files included in user-defined fileName #\r\n-# - Preprocessed files (alignment, ...) included in p x n dataframe #\r\n-################################################################################################\r\n-NmrBucketing <- function(fileType,fileName,leftBorder = 10.0,rightBorder = 0.5,bucketSize = 0.04,exclusionZones,\r\n- exclusionZonesBorders=NULL,graph=c("None","Overlay","One_per_individual"),\r\n- nomFichier,savLog.txtC = NULL) \r\n-{\r\n- ## Option\r\n- ##---------------\r\n- strAsFacL <- options()$stringsAsFactors\r\n- options(stingsAsFactors = FALSE)\r\n- options(warn = -1)\r\n- \r\n- \r\n- ## Constants\r\n- ##---------------\r\n- topEnvC <- environment()\r\n- flgC <- "\\n"\r\n- \r\n- ## Log file (in case of integration into Galaxy)\r\n- ##----------------------------------------------\r\n- if(!is.null(savLog.txtC))\r\n- sink(savLog.txtC, append = TRUE)\r\n- \r\n- ## Functions definition\r\n- ##--------------------- \r\n- ## RAW BRUKER FILE READING FUNCTION\r\n- NmRBrucker_read <- function(DataDir,SampleSpectrum)\r\n- {\r\n- \r\n- bruker.get_param <- function (ACQ,paramStr)\r\n- {\r\n- regexpStr <- paste("^...",paramStr,"=",sep="")\r\n- as.numeric(gsub("^[^=]+= ","" ,ACQ[which(simplify2array(regexpr(regexpStr,ACQ))>0)]))\r\n- }\r\n- \r\n- ACQFILE <- "acqus"\r\n- SPECFILE <- paste(DataDir,"/1r",sep="")\r\n- PROCFILE <- paste(DataDir,"/procs",sep="")\r\n- \r\n- ACQ <- readLines(ACQFILE)\r\n- TD <- bruker.get_param(ACQ,"TD")\r\n- SW <- bruker.get_param(ACQ,"SW")\r\n- SWH <- bruker.get_param(ACQ,"SW_h")\r\n- DTYPA <- bruker.get_param(ACQ,"DTYPA")\r\n- BYTORDA <- bruker.get_param(ACQ,"BYTORDA")\r\n- #ENDIAN = ifelse( BYTORDA==0, "little", "big")\r\n- ENDIAN <- "little"\r\n- SIZE = ifelse( DTYPA==0, 4, 8)\r\n- \r\n- PROC <- readLines(PROCFILE)\r\n- OFFSET <- bruker.get_param(PROC,"OFFSET")\r\n- SI <- bruker.get_param(PROC,"SI")\r\n- \r\n- to.read = file(SPECFILE,"rb")\r\n- maxTDSI = max(TD,SI)\r\n- # signal<-rev(readBin(to.read, what="int",size=SIZE, n=TD, signed = TRUE, endian = ENDIAN))\r\n- signal<-rev(readBin(to.read, what="int",size=SIZE, n=maxTDSI, signed = TRUE, endian = ENDIAN))\r\n- close(to.read)\r\n- \r\n- td <- length(signal)\r\n- \r\n- # dppm <- SW/(TD-1)\r\n- dppm <- SW/(td-1)\r\n- pmax <- OFFSET\r\n- pmin <- OFFSET - SW\r\n- ppmseq <- seq(from=pmin, to=pmax, by=dppm)\r\n- signal <- 100*signal/max(signal)\r\n- \r\n- SampleSpectrum <- cbind(ppmseq,signal)\r\n- return(SampleSpectrum)\r\n- }\r\n- \r\n- ## SPECTRUM BUCKETING\r\n- NmrBrucker_bucket <- function(spectrum)\r\n- {\r\n- # Initialisations\r\n- b <- 1\r\n- j <- 1\r\n- # Variable number\r\n- J <- round((spectrum[1,1]-spectrum[dim(spectrum)[1],1])/bucketSize)\r\n- f.bucket <- matrix(rep(0,J*2),ncol=2)\r\n- colnames(f.bucket) <- c("Bucket",FileNames[i])\r\n- \r\n- \r\n- # Data bucketing\r\n-'..b'Names <- list.files(fileName)\r\n- n <- length(FileNames)\r\n- \r\n- # Reading and Bucketing\r\n- fileName <- paste(fileName,"/",sep="")\r\n- \r\n- i <- 1\r\n- while (i <= n)\r\n- {\r\n- # File reading\r\n- SampleDir <- paste(fileName,FileNames[i],"/1/",sep="")\r\n- setwd(SampleDir)\r\n- DataDir <- "pdata/1"\r\n- \r\n- rawSpectrum <- NmRBrucker_read(DataDir,rawSpectrum)\r\n- \r\n- orderedSpectrum <- rawSpectrum[order(rawSpectrum[,1],decreasing=T), ]\r\n- \r\n- # Removal of chemical shifts > leftBorder or < rightBorder boundaries\r\n- truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]\r\n- truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)\r\n- \r\n- # Bucketing\r\n- spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)\r\n- ppm <- spectrum.bucket[,1]\r\n- \r\n- # spectrum Concatenation\r\n- if (i == 1)\r\n- bucketedSpectra <- spectrum.bucket\r\n- if (i > 1)\r\n- bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])\r\n- colnames(bucketedSpectra)[i+1] <- FileNames[i]\r\n- \r\n- # Next sample\r\n- rm(spectrum.bucket)\r\n- i <- i +1\r\n- }\r\n- # Directory\r\n- cd(fileName) \r\n- }\r\n- \r\n- ## Inputs from dataset (preprocessed files)\r\n- if (fileType=="tsv")\r\n- {\r\n- FileNames <- colnames(fileName)\r\n- n <- length(FileNames)\r\n- \r\n- for (i in 1:ncol(fileName))\r\n- {\r\n- orderedSpectrum <- cbind(as.numeric(rownames(fileName)),fileName[,i])\r\n- orderedSpectrum <- orderedSpectrum[order(orderedSpectrum[,1],decreasing=T), ]\r\n- \r\n- truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]\r\n- truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)\r\n- \r\n- # Bucketing\r\n- spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)\r\n- ppm <- spectrum.bucket[,1]\r\n- \r\n- # spectrum Concatenation\r\n- if (i == 1)\r\n- bucketedSpectra <- spectrum.bucket\r\n- if (i > 1)\r\n- bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])\r\n- colnames(bucketedSpectra)[i+1] <- colnames(fileName)[i]\r\n- }\r\n- }\r\n- \r\n- identifiants <- gsub("([- , * { } | \\\\[ ])","_",colnames(bucketedSpectra)[-1])\r\n- colnames(bucketedSpectra) <- c(colnames(bucketedSpectra)[1],identifiants)\r\n-\r\n- bucketedSpectra <- bucketedSpectra[bucketedSpectra[,1]!=0,]\r\n- rownames(bucketedSpectra) <- paste("B",bucketedSpectra[,1],sep="")\r\n- bucketedSpectra <- bucketedSpectra[,-1]\r\n- \r\n- # Metadata matrice outputs\r\n- sampleMetadata <- data.frame(1:n)\r\n- rownames(sampleMetadata) <- colnames(bucketedSpectra)\r\n- colnames(sampleMetadata) <- "SampleOrder"\r\n- \r\n- variableMetadata <- data.frame(1:nrow(bucketedSpectra))\r\n- rownames(variableMetadata) <- rownames(bucketedSpectra)\r\n- colnames(variableMetadata) <- "VariableOrder"\r\n-\r\n-\r\n- return(list(bucketedSpectra,sampleMetadata,variableMetadata,ppm)) # ,truncatedSpectrum_matrice\r\n-}\r\n-\r\n-\r\n-#################################################################################################################\r\n-## Typical function call\r\n-#################################################################################################################\r\n-## StudyDir <- "K:/PROJETS/Metabohub/Bruker/Tlse_BPASourisCerveau/"\r\n-## upper <- 9.5\r\n-## lower <- 0.8\r\n-## bucket.width <- 0.01\r\n-## exclusion <- TRUE\r\n-## exclusion.zone <- list(c(5.1,4.5))\r\n-## graphique <- "Overlay"\r\n-## nomFichier <- "Tlse_BPASourisCerveau_NmrBucketing_graph.pdf"\r\n-## tlse_cerveaupnd21.bucket <- NmrBucketing(StudyDir,upper,lower,bucket.width,exclusion,exclusion.zone,graphique,nomFichier)\r\n-## write.table(tlse_cerveaupnd21.bucket,file=paste(StudyDir,"Tlse_BPASourisCerveau_NmrBucketing_dataMatrix.tsv",sep=""),\r\n-## quote=FALSE,row.nmaes=FALSE,sep="\\t")\r\n-#################################################################################################################\r\n' |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/NmrBucketing_wrapper.R --- a/nmr_bucketing/NmrBucketing_wrapper.R Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,295 +0,0 @@\n-#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file\r\n-\r\n-## 070115_NmrBucketing2galaxy_v1.R\r\n-## Marie Tremblay-Franco\r\n-## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics\r\n-## www.metabohub.fr/en\r\n-## marie.tremblay-franco@toulouse.inra.fr\r\n-\r\n-runExampleL <- FALSE\r\n-\r\n-if(runExampleL) {\r\n-##------------------------------\r\n-## Example of arguments\r\n-##------------------------------\r\n-argLs <- list(StudyDir = "Tlse_BPASourisCerveau",\r\n- upper = "10.0",\r\n- lower = "0.50",\r\n- bucket.width = "0.01",\r\n- exclusion = "TRUE",\r\n- exclusion.zone = list(c(6.5,4.5)),\r\n- graph="Overlay")\r\n-\r\n-argLs <- c(argLs,\r\n- list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""),\r\n- sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""),\r\n- variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""),\r\n- graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""),\r\n- logOut = paste(directory,"_NmrBucketing_log.txt",sep="")))\r\n-}\r\n-\r\n-##------------------------------\r\n-## Options\r\n-##------------------------------\r\n-strAsFacL <- options()$stringsAsFactors\r\n-options(stringsAsFactors = FALSE)\r\n-\r\n-\r\n-##------------------------------\r\n-## Libraries laoding\r\n-##------------------------------\r\n-# For parseCommandArgs function\r\n-library(batch)\r\n-# For cumtrapz function\r\n-library(pracma)\r\n-\r\n-# R script call\r\n-source_local <- function(fname)\r\n-{\r\n-\targv <- commandArgs(trailingOnly = FALSE)\r\n-\tbase_dir <- dirname(substring(argv[grep("--file=", argv)], 8))\r\n-\tsource(paste(base_dir, fname, sep="/"))\r\n-}\r\n-#Import the different functions\r\n-source_local("NmrBucketing_script.R")\r\n-source_local("DrawSpec.R")\r\n-\r\n-##------------------------------\r\n-## Errors ?????????????????????\r\n-##------------------------------\r\n-\r\n-\r\n-##------------------------------\r\n-## Constants\r\n-##------------------------------\r\n-topEnvC <- environment()\r\n-flagC <- "\\n"\r\n-\r\n-\r\n-##------------------------------\r\n-## Script\r\n-##------------------------------\r\n-if(!runExampleL)\r\n- argLs <- parseCommandArgs(evaluate=FALSE)\r\n-\r\n-\r\n-## Parameters Loading\r\n-##-------------------\r\n- # Inputs\r\n-if (!is.null(argLs[["zipfile"]])){\r\n-\tfileType="zip"\r\n-\tzipfile= argLs[["zipfile"]]\r\n-\tdirectory=unzip(zipfile, list=F)\r\n-\tdirectory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")\r\n-} else if (!is.null(argLs[["tsvfile"]])){\r\n-\tfileType="tsv"\r\n-\tdirectory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\\t")\r\n-}\r\n-\r\n-leftBorder <- argLs[["left_border"]]\r\n-rightBorder <- argLs[["right_border"]]\r\n-bucketSize <- argLs[["bucket_width"]]\r\n-exclusionZones <- argLs[["zone_exclusion_choices.choice"]]\r\n-\r\n-exclusionZonesBorders <- NULL\r\n-if (!is.null(argLs$zone_exclusion_left))\r\n-{\r\n- for(i in which(names(argLs)=="zone_exclusion_left"))\r\n- {\r\n- exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))\r\n- }\r\n-}\r\n-\r\n-graphique <- argLs[["graphType"]]\r\n-\r\n- # Outputs\r\n-nomGraphe <- argLs[["graphOut"]]\r\n-dataMatrixOut <- argLs[["dataMatrixOut"]]\r\n-logFile <- argLs[["logOut"]]\r\n-if (fileType=="zip")\r\n-{\r\n- sampleMetadataOut <- argLs[["sampleOut"]]\r\n- variableMetadataOut <- argLs[["variableOut"]]\r\n-}\r\n-\r\n-## Checking arguments\r\n-##-------------------\r\n-error.stock <- "\\n"\r\n-\r\n-if(length(error.stock) > 1)\r\n- stop(error.stock)\r\n-\r\n-\r\n-## Computation\r\n-##------------\r\n-outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize,\r\n-\t\t\t\t\t\texclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe,\r\n-\t\t\t\t\t\tsavLog.txtC=logFile)\r\n-data_bucket <- outputs[[1]]\r\n-data_sample <- outputs[[2]]\r\n-data_variable <- outputs[[3]]\r\n-ppm <- outputs[[4]]\r\n-ppm <- round(ppm,2)\r\n-\r\n-## G'..b'):nrow(data_bucket),]))\r\n- drawSpec(spectra,xlab="", ylab="Intensity", main="")\r\n- }\r\n- }\r\n- else\r\n- {\r\n- for (i in 1:ncol(data_bucket))\r\n- {\r\n- par(mfrow=c((nbZones+2),1))\r\n- n <- length(excludedZone)\r\n- spectra <- t(data_bucket[,i])\r\n-\t names(spectra) <- rownames(data_bucket)\r\n- plot(1:length(spectra), spectra, type=\'l\', xlab="", ylab="Intensity", main=colnames(data_bucket)[i], xaxt = "n")\r\n-\t xPos <- 1\r\n-\t nAxisPos <- 4\r\n-\t startP <- length(nAxisPos) \r\n-\t endP <- nrow(data_bucket)\r\n-\t GraphRange <- c(startP:endP)\r\n-\t tempVal = trunc(length(GraphRange)/nAxisPos)\r\n-\t xPos = c(0:nAxisPos) * tempVal\r\n-\t axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])\r\n- \r\n- ## Zoomed spectral window depending on exclusion zone(s)\r\n- if (nbZones != 0)\r\n- {\r\n- BInf <- excludedZone[n]\r\n- if (round(BInf,1) == BInf)\r\n- {\r\n- BInf <- BInf+0.01\r\n- }\r\n- spectra <- t(data_bucket[1:(which(ppm == BInf)[[1]]),i])\r\n-\t\tnames(spectra) <- rownames(data_bucket)[1:(which(ppm == BInf)[[1]])]\r\n-\t\tplot(1:length(spectra), spectra, type=\'l\',xlab="", ylab="Intensity", main="", xaxt = "n")\t\t\t\r\n-\t\txPos <- 1\r\n-\t\tnAxisPos <- 4\r\n-\t\tstartP <- length(nAxisPos) \r\n-\t\tendP <- length(spectra)\r\n-\t\tGraphRange <- c(startP:endP)\r\n-\t\ttempVal = trunc(length(GraphRange)/nAxisPos)\r\n-\t\txPos = c(0:nAxisPos) * tempVal\r\n-\t\taxis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])\r\n- n <- n - 1\r\n- \r\n- while (n >= nbZones & nbZones > 1)\r\n- {\r\n- BInf <- excludedZone[n-1]\r\n- if (round(BInf,1) > BInf)\r\n- {\r\n- BInf <- BInf+0.01\r\n- }\r\n- spectra <- t(data_bucket[(which(ppm == excludedZone[n])[[1]]):(which(ppm == BInf)[[1]]),i])\r\n-\t\t names(spectra) <- rownames(data_bucket)[(which(ppm == excludedZone[n])[[1]]):(which(ppm == BInf)[[1]])]\r\n- plot(1:length(spectra), spectra, type=\'l\',xlab="", ylab="Intensity", main="", xaxt = "n")\r\n-\t\t xPos <- 1\r\n-\t\t nAxisPos <- 4\r\n-\t\t startP <- length(nAxisPos) \r\n-\t\t endP <- length(spectra)\r\n-\t\t GraphRange <- c(startP:endP)\r\n-\t\t tempVal = trunc(length(GraphRange)/nAxisPos)\r\n-\t\t xPos = c(0:nAxisPos) * tempVal\r\n-\t\t axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])\r\n- n <- n - 2\r\n- }\r\n- \r\n- BInf <- excludedZone[1]\r\n- if (round(BInf,1) <= BInf)\r\n- {\r\n- BInf <- BInf+0.01\r\n- }\r\n- spectra <- t(data_bucket[(which(ppm == BInf)[[1]]):nrow(data_bucket),i])\r\n-\t\tnames(spectra) <- rownames(data_bucket)[(which(ppm == BInf)[[1]]):nrow(data_bucket)]\r\n- plot(1:length(spectra), spectra, type=\'l\',xlab="", ylab="Intensity", main="", xaxt = "n")\r\n-\t\txPos <- 1\r\n-\t\tnAxisPos <- 4\r\n-\t\tstartP <- length(nAxisPos) \r\n-\t\tendP <- length(spectra)\r\n-\t\tGraphRange <- c(startP:endP)\r\n-\t\ttempVal = trunc(length(GraphRange)/nAxisPos)\r\n-\t\txPos = c(0:nAxisPos) * tempVal\r\n-\t\taxis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])\r\n- }\r\n- }\r\n- }\r\n- dev.off()\r\n-}\r\n-## Saving\r\n-##-------\r\n- # Data\r\n-data_bucket <- cbind(rownames(data_bucket),data_bucket)\r\n-colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1])\r\n-write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\\t")\r\n- # Sample\r\n-data_sample <- cbind(rownames(data_sample),data_sample)\r\n-colnames(data_sample) <- c("Sample",colnames(data_sample)[-1])\r\n-write.table(data_sample,file=argLs$sampleOut,quote=FALSE,row.names=FALSE,sep="\\t")\r\n- # Variable\r\n-data_variable <- cbind(rownames(data_variable),data_variable)\r\n-colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1])\r\n-write.table(data_variable,file=argLs$variableOut,quote=FALSE,row.names=FALSE,sep="\\t")\r\n-\r\n-\r\n-## Ending\r\n-##---------------------\r\n-\r\n-cat("\\nEnd of \'NMR bucketing\' Galaxy module call: ", as.character(Sys.time()), sep = "")\r\n-\r\n-## sink(NULL)\r\n-\r\n-options(stringsAsFactors = strAsFacL)\r\n-\r\n-rm(list = ls())\r\n' |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/NmrBucketing_xml.xml --- a/nmr_bucketing/NmrBucketing_xml.xml Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,293 +0,0 @@\n-<tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.3">\r\n-\r\n- <description> Bucketing and integration of NMR Bruker raw data</description>\r\n-\r\n- <requirements>\r\n-\t <requirement type="package" version="1.1_4">r-batch</requirement>\r\n-\t <requirement type="package" version="1.8.8">r-pracma</requirement>\r\n- </requirements>\r\n-\r\n- <stdio>\r\n- <exit_code range="1:" level="fatal" />\r\n- </stdio>\r\n-\r\n- <command>\r\n- Rscript \'$__tool_directory__/NmrBucketing_wrapper.R\'\r\n-\r\n- #if $inputs.input == "tsv_file":\r\n- tsvfile \'$inputs.tsv_file\'\r\n- #elif $inputs.input == "zip_file":\r\n- zipfile \'$inputs.zip_file\'\r\n- #end if\r\n-\r\n-\r\n- ## Bucket width\r\n- bucket_width $bucket_width\r\n-\r\n- ## Spectra borders\r\n- left_border $left_border\r\n- right_border $right_border\r\n-\r\n-\r\n- ## Spectra representation\r\n- graphType $graphType\r\n-\r\n- ## Exclusion zone\r\n- zone_exclusion_choices.choice ${zone_exclusion_choices.choice}\r\n- #if str($zone_exclusion_choices.choice) == \'yes\':\r\n- #for $i in $zone_exclusion_choices.conditions:\r\n- zone_exclusion_left ${i.zone_exclusion_left}\r\n- zone_exclusion_right ${i.zone_exclusion_right}\r\n- #end for\r\n- #end if\r\n-\r\n- ## Outputs\r\n- logOut log.log\r\n- dataMatrixOut \'$dataMatrixOut\'\r\n- sampleOut \'$sampleOut\'\r\n- variableOut \'$variableOut\'\r\n- graphOut \'$graphOut\'; cat log.log\r\n- </command>\r\n-\r\n- <inputs>\r\n- <conditional name="inputs">\r\n- <param name="input" type="select" label="Choose your inputs method" >\r\n- <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>\r\n- <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option>\r\n- </param>\r\n- <when value="zip_file">\r\n- <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />\r\n- </when>\r\n- <when value="tsv_file">\r\n- <param name="tsv_file" type="data" format="tabular" label="Tsv file" />\r\n- </when>\r\n- </conditional>\r\n-\r\n- <param name="bucket_width" label="Bucket width" type="float" value="0.04" help="Default value is 0.04 ppm"/>\r\n-\r\n- <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>\r\n- <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>\r\n-\r\n- <conditional name="zone_exclusion_choices">\r\n- <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >\r\n- <option value="yes" > yes </option>\r\n- <option value="no" selected="true"> no </option>\r\n- </param>\r\n- <when value="yes">\r\n- <repeat name="conditions" title="exclusion zones">\r\n- <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />\r\n- <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />\r\n- </repeat>\r\n- </when>\r\n- <when value="no">\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-\r\n- </inputs>\r\n-\r\n- <outputs>\r\n- '..b'-------------------+----------------------+--------+\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-| 1 : Choose your inputs | zip |\r\n-+---------------------------+------------+\r\n-| 1 : Choose your inputs | tsv |\r\n-+---------------------------+------------+\r\n-\r\n-**Choose your inputs**\r\n-\r\n-You have three methods for your inputs:\r\n-\r\n-| Zip file (recommended): You can put a zip file containing your inputs as raw Bruker files: myinputs.zip (containing all your conditions as sub-directories).\r\n-| Tsv file: You can put a tsv file containing your inputs as preprocessed spectra: myinputs.tsv (containing all your conditions in columns and chemical shifts in rows).\r\n-\r\n-.. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png\r\n-:width: 800\r\n-\r\n-----------\r\n-Parameters\r\n-----------\r\n-\r\n-Bucket width\r\n-| size of windows\r\n-|\r\n-\r\n-Left limit\r\n-| Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm\r\n-|\r\n-\r\n-Right limit\r\n-| Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm\r\n-|\r\n-\r\n-Exclusion zone(s)\r\n-| Spectral regions to exclude, water, solvents, ... resonance\r\n-| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,\r\n-| If NO: no zone to exclude\r\n-| Default value is NO\r\n-|\r\n-\r\n-Left exclusion zone\r\n-| Upper boundary of exclusion zone\r\n-|\r\n-\r\n-Right exclusion zone\r\n-| Lower boundary of exclusion zone\r\n-\r\n-| *Notes:*\r\n-| - these parameters can be used several times using the "Add new exclusion zones" button\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-bucketedData.tsv\r\n-| tabular output\r\n-| Data matrix with p rows (buckets) and n columns (samples) containing the intensities\r\n-|\r\n-\r\n-sampleMetadata.tsv\r\n-| tabular output\r\n-| file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order: the rownames of sampleMetadata must be identical to the colnames of the bucketedData. Can add columns with numeric and/or character sample metadata. This file is optional in the normalization step and mandatory in the statistical analysis step of the workflow.\r\n-|\r\n-\r\n-variableMetadata.tsv\r\n-| tabular output\r\n-| file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order: the rownames of variableMetadata must be identical to the rownames of the bucketedData. Can add columns with numeric and/or character variable metadata. This file is mandatory in the statistical analysis step of the workflow.\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-Changelog/News\r\n---------------\r\n-\r\n-**Version 1.0.3 - 24/10/2016**\r\n-\r\n-- ENHANCEMENT: add possibility of bucketing processed files (upstream tools)\r\n-\r\n-**Version 1.0.2 - 12/08/2016**\r\n-\r\n-- ENHANCEMENT: x-axis customization: add chemical shift labels\r\n-\r\n-**Version 1.0.1 - 04/04/2016**\r\n-\r\n-- TEST: refactoring to pass planemo test using conda dependencies\r\n-\r\n-\r\n-**Version 2015-01-08 - 08/01/2015**\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 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/README.rst --- a/nmr_bucketing/README.rst Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,28 +0,0 @@ - -Changelog/News --------------- - -**Version 1.0.3 - 24/10/2016** - -- ENHANCEMENT: add possibility of bucketing processed files (upstream tools) - -**Version 1.0.2 - 12/08/2016** - -- ENHANCEMENT: x-axis customization: add chemical shift labels - -**Version 1.0.1 - 04/04/2016** - -- TEST: refactoring to pass planemo test using conda dependencies - - -**Version 2015-01-08 - 08/01/2015** - - - -Test Status ------------ - -Planemo test using conda: passed - -Planemo shed_test: passed - |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/planemo_test.sh --- a/nmr_bucketing/planemo_test.sh Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -planemo conda_init -planemo conda_install . -planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev" - -#All 1 test(s) executed passed. -#nmr_bucketing[0]: passed - - -planemo shed_test -t testtoolshed --install_galaxy --galaxy_branch "dev" - -#All 1 test(s) executed passed. -#testtoolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/nmr_bucketing/NmrBucketing/1.0.1[0]: passed |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/repository_dependencies.xml --- a/nmr_bucketing/repository_dependencies.xml Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories> - <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> |
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| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/test-data/MTBLS1_bucketedData.tabular --- a/nmr_bucketing/test-data/MTBLS1_bucketedData.tabular Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,595 +0,0 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|
| b |
| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/test-data/MTBLS1_sampleMetadata.tabular --- a/nmr_bucketing/test-data/MTBLS1_sampleMetadata.tabular Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -Sample SampleOrder -ADG10003u_007 1 -ADG10003u_008 2 -ADG10003u_009 3 -ADG10003u_010 4 -ADG10003u_015 5 -ADG10003u_016 6 -ADG10003u_017 7 -ADG10003u_021 8 -ADG10003u_022 9 -ADG10003u_023 10 -ADG10003u_051 11 -ADG10003u_052 12 -ADG10003u_053 13 -ADG10003u_066 14 -ADG10003u_067 15 -ADG10003u_071 16 -ADG10003u_072 17 -ADG10003u_073 18 -ADG10003u_087 19 -ADG10003u_088 20 -ADG10003u_089 21 -ADG10003u_097 22 -ADG10003u_098 23 |
| b |
| diff -r 3cd762aac7a4 -r 966fcf7ae66e nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular --- a/nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular Thu Apr 20 08:53:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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-B0.846 589 -B0.836 590 -B0.826 591 -B0.816 592 -B0.806 593 -B0.8 594 |
| b |
| diff -r 3cd762aac7a4 -r 966fcf7ae66e planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Thu Oct 26 06:01:14 2017 -0400 |
| [ |
| @@ -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 3cd762aac7a4 -r 966fcf7ae66e test-data/MTBLS1_bucketedData.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_bucketedData.tabular Thu Oct 26 06:01:14 2017 -0400 |
| b |
| b'@@ -0,0 +1,595 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|
| b |
| diff -r 3cd762aac7a4 -r 966fcf7ae66e test-data/MTBLS1_bucketedData_normalized.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_bucketedData_normalized.tabular Thu Oct 26 06:01:14 2017 -0400 |
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