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nmr_bucketing/.shed.yml 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 nmr_bucketing/tool_dependencies.xml |
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MANUAL_INSTALL.txt NmrBucketing_script.R NmrBucketing_wrapper.R NmrBucketing_xml.xml README.rst planemo_test.sh repository_dependencies.xml static/images/MTH - Architecture repertoire Bruker.png static/images/Mth_Travaux.png test-data/MTBLS1.zip test-data/MTBLS1_bucketedData.tabular test-data/MTBLS1_sampleMetadata.tabular test-data/MTBLS1_variableMetadata.tabular tool_dependencies.xml |
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diff -r d61f6ceef5d6 -r 475d219739ff MANUAL_INSTALL.txt --- a/MANUAL_INSTALL.txt Tue Nov 22 05:22:03 2016 -0500 +++ /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/$library - -## --- XML help part --- ## -one image: -Copy the 'Mth_Architecture_Repertoire_Bruker.png' file within the directory to your galaxy-dist/static/images/ - - - - Activate the "user_library_import_dir" in your /galaxy/dist/galaxy-dist/universe_wsgi.ini and create the users directories in this path, for example: - - #In universe_wsgi.ini - user_library_import_dir = /projet/sbr/galaxy/import/user - - #Create the user "myaccount" in this path - - User path: /projet/sbr/galaxy/import/user/myaccount@sb-roscoff.fr - - - - -Finally, restart Galaxy \ No newline at end of file |
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diff -r d61f6ceef5d6 -r 475d219739ff NmrBucketing_script.R --- a/NmrBucketing_script.R Tue Nov 22 05:22:03 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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b'@@ -1,283 +0,0 @@\n-################################################################################################\r\n-# SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES #\r\n-# User : Galaxy #\r\n-# Original data : -- #\r\n-# Starting date : 20-10-2014 #\r\n-# Version 1 : 18-12-2014 #\r\n-# Version 2 : 07-01-2015 #\r\n-# Version 3 : 24-10-2016 #\r\n-# #\r\n-# Input files : modification on october 2016 #\r\n-# - Raw bruker files included in user-defined fileName #\r\n-# - Preprocessed files (alignment, ...) included in p x n dataframe #\r\n-################################################################################################\r\n-NmrBucketing <- function(fileType,fileName,leftBorder = 10.0,rightBorder = 0.5,bucketSize = 0.04,exclusionZones,\r\n- exclusionZonesBorders=NULL,graph=c("None","Overlay","One_per_individual"),\r\n- nomFichier,savLog.txtC = NULL) \r\n-{\r\n- ## Option\r\n- ##---------------\r\n- strAsFacL <- options()$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'rum.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- \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- # Bucketed spectra graph\r\n- if (graph != "None")\r\n- {\r\n- # Graphic Device opening\r\n- pdf(nomFichier,onefile=TRUE)\r\n-\r\n- if (graph == "Overlay")\r\n- {\r\n- x <- 1:length(bucketedSpectra[,1])\r\n- ymax <- max(bucketedSpectra)\r\n- plot(x,bucketedSpectra[,1],ylim=c(0,ymax),type=\'l\',col=1,xlab="",xaxt="n",ylab="Intensity")\r\n- # x-axis labels\r\n- axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2)\r\n- for (i in 2:ncol(bucketedSpectra))\r\n- {\r\n- spectre <- bucketedSpectra[,i]\r\n- lines(spectre,col=i)\r\n- }\r\n-# legend(0,ymax,lty=c(1,1),legend=colnames(bucketedSpectra),col=1:ncol(bucketedSpectra))\r\n- }\r\n- else\r\n- {\r\n- for (i in 1:ncol(bucketedSpectra))\r\n- {\r\n- x <- 1:length(bucketedSpectra[,1])\r\n- plot(x,bucketedSpectra[,i],type=\'l\',col=1,xlab="",xaxt="n",ylab="Intensity")\r\n- axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2)\r\n- }\r\n- }\r\n- dev.off()\r\n- }\r\n- return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,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 d61f6ceef5d6 -r 475d219739ff NmrBucketing_wrapper.R --- a/NmrBucketing_wrapper.R Tue Nov 22 05:22:03 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,163 +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 - -if(runExampleL) { -##------------------------------ -## Example of arguments -##------------------------------ -argLs <- list(StudyDir = "Tlse_BPASourisCerveau", - upper = "10.0", - lower = "0.50", - bucket.width = "0.01", - exclusion = "TRUE", - exclusion.zone = list(c(6.5,4.5)), - graph="Overlay") - -argLs <- c(argLs, - list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""), - sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""), - variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""), - graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""), - logOut = paste(directory,"_NmrBucketing_log.txt",sep=""))) -} - -##------------------------------ -## Options -##------------------------------ -strAsFacL <- options()$stringsAsFactors -options(stringsAsFactors = FALSE) - - -##------------------------------ -## Libraries laoding -##------------------------------ -# For parseCommandArgs function -library(batch) -# For cumtrapz function -library(pracma) - -# R script call -source_local <- function(fname) -{ - argv <- commandArgs(trailingOnly = FALSE) - base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) - source(paste(base_dir, fname, sep="/")) -} -#Import the different functions -source_local("NmrBucketing_script.R") - -##------------------------------ -## Errors ????????????????????? -##------------------------------ - - -##------------------------------ -## Constants -##------------------------------ -topEnvC <- environment() -flagC <- "\n" - - -##------------------------------ -## Script -##------------------------------ -if(!runExampleL) - argLs <- parseCommandArgs(evaluate=FALSE) - -## sink(argLs[["logOut"]]) - - -## Parameters Loading -##------------------- - # Inputs -if (!is.null(argLs[["zipfile"]])){ - fileType="zip" - zipfile= argLs[["zipfile"]] - directory=unzip(zipfile, list=F) - directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") -} else if (!is.null(argLs[["library"]])){ - fileType="zip" - directory=argLs[["library"]] - if(!file.exists(directory)){ - error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.") - print(error_message) - stop(error_message) - } -} else if (!is.null(argLs[["tsvfile"]])){ - fileType="tsv" - directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t") -} - -leftBorder <- argLs[["left_border"]] -rightBorder <- argLs[["right_border"]] -bucketSize <- argLs[["bucket_width"]] -exclusionZones <- argLs[["zone_exclusion_choices.choice"]] - -exclusionZonesBorders <- NULL -if (!is.null(argLs$zone_exclusion_left)) -{ - for(i in which(names(argLs)=="zone_exclusion_left")) - { - exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) - } -} - -graphique <- argLs[["graphType"]] - - # Outputs -nomGraphe <- argLs[["graphOut"]] -dataMatrixOut <- argLs[["dataMatrixOut"]] -sampleMetadataOut <- argLs[["sampleOut"]] -variableMetadataOut <- argLs[["variableOut"]] -logFile <- argLs[["logOut"]] - -## Checking arguments -##------------------- -error.stock <- "\n" - -if(length(error.stock) > 1) - stop(error.stock) - - -## Computation -##------------ -outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize, - exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe, - savLog.txtC=logFile) -data_bucket <- outputs[[1]] -data_sample <- outputs[[2]] -data_variable <- outputs[[3]] - -## Saving -##------- - # Data -data_bucket <- cbind(rownames(data_bucket),data_bucket) -colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1]) -write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t") - # Sample -data_sample <- cbind(rownames(data_sample),data_sample) -colnames(data_sample) <- c("Sample",colnames(data_sample)[-1]) -write.table(data_sample,file=argLs$sampleOut,quote=FALSE,row.names=FALSE,sep="\t") - # Variable -data_variable <- cbind(rownames(data_variable),data_variable) -colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1]) -write.table(data_variable,file=argLs$variableOut,quote=FALSE,row.names=FALSE,sep="\t") - - -## Ending -##--------------------- - -cat("\nEnd of 'NMR bucketing' Galaxy module call: ", as.character(Sys.time()), sep = "") - -## sink(NULL) - -options(stringsAsFactors = strAsFacL) - -rm(list = ls()) |
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diff -r d61f6ceef5d6 -r 475d219739ff NmrBucketing_xml.xml --- a/NmrBucketing_xml.xml Tue Nov 22 05:22:03 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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b'@@ -1,304 +0,0 @@\n-<tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.3">\r\n-\r\n- <description> Bucketing and integration of NMR Bruker raw data</description>\r\n-\r\n- <requirements>\r\n-\t <requirement type="package" version="1.1_4">r-batch</requirement>\r\n-\t <requirement type="package" version="1.8.8">r-pracma</requirement>\r\n- </requirements>\r\n-\r\n- <stdio>\r\n- <exit_code range="1:" level="fatal" />\r\n- </stdio>\r\n-\r\n- <command>\r\n- Rscript \'$__tool_directory__/NmrBucketing_wrapper.R\'\r\n-\r\n- #if $inputs.input == "lib":\r\n- library \'$__app__.config.user_library_import_dir/$__user_email__/$inputs.library\'\r\n- #elif $inputs.input == "tsv_file":\r\n- tsvfile \'$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- <option value="lib" >Library directory name</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- <when value="lib">\r\n- <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >\r\n- <validator type="empty_field"/> \r\n- </param>\r\n- </when>\r\n-\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'..b'+------------+\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-| library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain 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)\t \r\n-\t \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-\r\n' |
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diff -r d61f6ceef5d6 -r 475d219739ff README.rst --- a/README.rst Tue Nov 22 05:22:03 2016 -0500 +++ /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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/.shed.yml Thu Mar 02 10:24:34 2017 -0500 |
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@@ -0,0 +1,7 @@ +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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/MANUAL_INSTALL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/MANUAL_INSTALL.txt Thu Mar 02 10:24:34 2017 -0500 |
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@@ -0,0 +1,59 @@ +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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/NmrBucketing_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/NmrBucketing_script.R Thu Mar 02 10:24:34 2017 -0500 |
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b'@@ -0,0 +1,254 @@\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'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+ 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+ ## OUTPUTS\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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/NmrBucketing_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/NmrBucketing_wrapper.R Thu Mar 02 10:24:34 2017 -0500 |
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@@ -0,0 +1,241 @@ +#!/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 + +if(runExampleL) { +##------------------------------ +## Example of arguments +##------------------------------ +argLs <- list(StudyDir = "Tlse_BPASourisCerveau", + upper = "10.0", + lower = "0.50", + bucket.width = "0.01", + exclusion = "TRUE", + exclusion.zone = list(c(6.5,4.5)), + graph="Overlay") + +argLs <- c(argLs, + list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""), + sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""), + variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""), + graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""), + logOut = paste(directory,"_NmrBucketing_log.txt",sep=""))) +} + +##------------------------------ +## Options +##------------------------------ +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + + +##------------------------------ +## Libraries laoding +##------------------------------ +# For parseCommandArgs function +library(batch) +# For cumtrapz function +library(pracma) + +# 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("NmrBucketing_script.R") +source_local("DrawSpec.R") + +##------------------------------ +## Errors ????????????????????? +##------------------------------ + + +##------------------------------ +## Constants +##------------------------------ +topEnvC <- environment() +flagC <- "\n" + + +##------------------------------ +## Script +##------------------------------ +if(!runExampleL) + argLs <- parseCommandArgs(evaluate=FALSE) + +## sink(argLs[["logOut"]]) + + +## Parameters Loading +##------------------- + # Inputs +if (!is.null(argLs[["zipfile"]])){ + fileType="zip" + zipfile= argLs[["zipfile"]] + directory=unzip(zipfile, list=F) + directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") +} else if (!is.null(argLs[["library"]])){ + fileType="zip" + directory=argLs[["library"]] + if(!file.exists(directory)){ + error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.") + print(error_message) + stop(error_message) + } +} else if (!is.null(argLs[["tsvfile"]])){ + fileType="tsv" + directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t") +} + +leftBorder <- argLs[["left_border"]] +rightBorder <- argLs[["right_border"]] +bucketSize <- argLs[["bucket_width"]] +exclusionZones <- argLs[["zone_exclusion_choices.choice"]] + +exclusionZonesBorders <- NULL +if (!is.null(argLs$zone_exclusion_left)) +{ + for(i in which(names(argLs)=="zone_exclusion_left")) + { + exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) + } +} + +graphique <- argLs[["graphType"]] + + # Outputs +nomGraphe <- argLs[["graphOut"]] +dataMatrixOut <- argLs[["dataMatrixOut"]] +logFile <- argLs[["logOut"]] +if (fileType=="zip") +{ + sampleMetadataOut <- argLs[["sampleOut"]] + variableMetadataOut <- argLs[["variableOut"]] +} + +## Checking arguments +##------------------- +error.stock <- "\n" + +if(length(error.stock) > 1) + stop(error.stock) + + +## Computation +##------------ +outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize, + exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe, + savLog.txtC=logFile) +data_bucket <- outputs[[1]] +data_sample <- outputs[[2]] +data_variable <- outputs[[3]] +ppm <- outputs[[4]] +ppm <- round(ppm,2) + +## Graphical outputs +##------------------ +if (graphique != "None") +{ + excludedZone <- NULL + for (c in 1:length(exclusionZonesBorders)) + { + excludedZone <- c(excludedZone,exclusionZonesBorders[[c]]) + excludedZone <- sort(excludedZone) + } + nbZones <- length(excludedZone)/2 + n <- length(excludedZone) + + # Graphic Device opening + pdf(nomGraphe,onefile=TRUE) + + if (graphique == "Overlay") + { + # Global spectral window + spectra <- data.frame(t(data_bucket)) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + + ## Zoomed spectral window depending on exclusion zone(s) + if (nbZones != 0) + { + spectra <- data.frame(t(data_bucket[1:(which(ppm == excludedZone[n])[[1]]),])) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + n <- n - 1 + + while (n >= nbZones & nbZones > 1) + { + spectra <- data.frame(t(data_bucket[(which(ppm == excludedZone[n])[[1]]):(which(ppm == excludedZone[n-1])[[1]]),])) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + n <- n - 2 + } + spectra <- data.frame(t(data_bucket[(which(ppm == excludedZone[1])[[1]]):nrow(data_bucket),])) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + } + } + else + { + for (i in 1:ncol(data_bucket)) + { + par(mfrow=c((nbZones+2),1)) + n <- length(excludedZone) + spectra <- t(data_bucket[,i]) + drawSpec(spectra,xlab="", ylab="Intensity", main=colnames(data_bucket)[i]) + + ## Zoomed spectral window depending on exclusion zone(s) + if (nbZones != 0) + { + spectra <- t(data_bucket[1:(which(ppm == excludedZone[n])[[1]]),i]) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + n <- n - 1 + + while (n >= nbZones & nbZones > 1) + { + spectra <- t(data_bucket[(which(ppm == excludedZone[n])[[1]]):(which(ppm == excludedZone[n-1])[[1]]),i]) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + n <- n - 2 + } + + spectra <- t(data_bucket[(which(ppm == excludedZone[1])[[1]]):nrow(data_bucket),i]) + drawSpec(spectra,xlab="", ylab="Intensity", main="") + } + } + } + dev.off() +} + +## Saving +##------- + # Data +data_bucket <- cbind(rownames(data_bucket),data_bucket) +colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1]) +write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t") +if (fileType=="zip") +{ + # Sample + data_sample <- cbind(rownames(data_sample),data_sample) + colnames(data_sample) <- c("Sample",colnames(data_sample)[-1]) + write.table(data_sample,file=argLs$sampleOut,quote=FALSE,row.names=FALSE,sep="\t") + # Variable + data_variable <- cbind(rownames(data_variable),data_variable) + colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1]) + write.table(data_variable,file=argLs$variableOut,quote=FALSE,row.names=FALSE,sep="\t") +} + +## Ending +##--------------------- + +cat("\nEnd of 'NMR bucketing' Galaxy module call: ", as.character(Sys.time()), sep = "") + +## sink(NULL) + +options(stringsAsFactors = strAsFacL) + +rm(list = ls()) |
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diff -r d61f6ceef5d6 -r 475d219739ff nmr_bucketing/NmrBucketing_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/NmrBucketing_xml.xml Thu Mar 02 10:24:34 2017 -0500 |
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b'@@ -0,0 +1,308 @@\n+<tool id="NmrBucketing" name="NMR_Bucketing" version="2.0.1">\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 $inputs.input == "lib":\r\n+ library \'$__app__.config.user_library_import_dir/$__user_email__/$inputs.library\'\r\n+ #elif $inputs.input == "tsv_file":\r\n+ tsvfile \'$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+ <option value="lib" >Library directory name</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+ <when value="lib">\r\n+ <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >\r\n+ <validator type="empty_field"/> \r\n+ </param>\r\n+ </when>\r\n+\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'..b'+------------+\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+| library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain 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)\t \r\n+\t \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+\r\n' |
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diff -r d61f6ceef5d6 -r 475d219739ff nmr_bucketing/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/README.rst Thu Mar 02 10:24:34 2017 -0500 |
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@@ -0,0 +1,28 @@ + +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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/planemo_test.sh Thu Mar 02 10:24:34 2017 -0500 |
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@@ -0,0 +1,12 @@ +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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/repository_dependencies.xml Thu Mar 02 10:24:34 2017 -0500 |
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@@ -0,0 +1,4 @@ +<?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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/test-data/MTBLS1.zip |
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diff -r d61f6ceef5d6 -r 475d219739ff nmr_bucketing/test-data/MTBLS1_bucketedData.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/test-data/MTBLS1_bucketedData.tabular Thu Mar 02 10:24:34 2017 -0500 |
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b |
diff -r d61f6ceef5d6 -r 475d219739ff nmr_bucketing/test-data/MTBLS1_sampleMetadata.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/test-data/MTBLS1_sampleMetadata.tabular Thu Mar 02 10:24:34 2017 -0500 |
b |
@@ -0,0 +1,24 @@ +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 d61f6ceef5d6 -r 475d219739ff nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular Thu Mar 02 10:24:34 2017 -0500 |
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+B0.846 589 +B0.836 590 +B0.826 591 +B0.816 592 +B0.806 593 +B0.8 594 |
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diff -r d61f6ceef5d6 -r 475d219739ff nmr_bucketing/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/tool_dependencies.xml Thu Mar 02 10:24:34 2017 -0500 |
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@@ -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-pracma" version="1.8.8"> + <repository changeset_revision="48eb1ff95b33" name="package_r_pracma_1_8_8" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
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diff -r d61f6ceef5d6 -r 475d219739ff planemo_test.sh --- a/planemo_test.sh Tue Nov 22 05:22:03 2016 -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 --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 d61f6ceef5d6 -r 475d219739ff repository_dependencies.xml --- a/repository_dependencies.xml Tue Nov 22 05:22:03 2016 -0500 +++ /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 d61f6ceef5d6 -r 475d219739ff static/images/MTH - Architecture repertoire Bruker.png |
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diff -r d61f6ceef5d6 -r 475d219739ff static/images/Mth_Travaux.png |
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diff -r d61f6ceef5d6 -r 475d219739ff test-data/MTBLS1.zip |
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diff -r d61f6ceef5d6 -r 475d219739ff test-data/MTBLS1_bucketedData.tabular --- a/test-data/MTBLS1_bucketedData.tabular Tue Nov 22 05:22:03 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,595 +0,0 @@\n-Bucket\tADG10003u_007\tADG10003u_008\tADG10003u_009\tADG10003u_010\tADG10003u_015\tADG10003u_016\tADG10003u_017\tADG10003u_021\tADG10003u_022\tADG10003u_023\tADG10003u_051\tADG10003u_052\tADG10003u_053\tADG10003u_066\tADG10003u_067\tADG10003u_071\tADG10003u_072\tADG10003u_073\tADG10003u_087\tADG10003u_088\tADG10003u_089\tADG10003u_097\tADG10003u_098\n-B9.295\t1.79949423217956e-06\t1.36845276225836e-05\t2.01160697683997e-05\t7.25986492795804e-07\t2.42490464839257e-05\t3.11580892214512e-05\t8.19866824235026e-06\t3.09192259268499e-05\t2.64389193821353e-05\t1.45055826888266e-05\t3.45040700032625e-06\t1.60970199365859e-05\t1.05993065753594e-05\t2.90248760646802e-05\t1.06130409475137e-05\t5.2278556041205e-06\t2.44519080406605e-05\t3.7420635381202e-05\t1.57230624459948e-05\t2.75224138622866e-06\t2.08828714579133e-05\t5.49917968773367e-05\t8.22464110337308e-06\n-B9.286\t0.000183987136571742\t4.73741598311689e-05\t6.48220850387143e-05\t4.08486623139604e-05\t0.000124595459054319\t3.41874426311483e-05\t0.000122371178407348\t3.49547713922308e-05\t0.00015628757744243\t2.37737814473545e-05\t5.13987818577577e-05\t0.000134108924379129\t9.59219627606648e-05\t8.44451844992086e-05\t0.00022720535031565\t9.86157895513715e-05\t1.06199525078497e-05\t3.70983827911379e-05\t3.16119098225048e-05\t5.1709215131723e-06\t2.21703993321988e-05\t1.19479684646357e-05\t8.95607890845055e-06\n-B9.276\t6.1185692617288e-05\t0.00020732837726723\t0.00012538786536446\t2.84181782334477e-05\t2.53083682825459e-05\t2.76930477756038e-05\t9.7914592965261e-05\t1.44908072132008e-05\t7.76504143484867e-05\t2.21918164602678e-05\t0.000443221195814841\t0.00034996670727668\t0.000412632862820386\t0.000146364982064243\t0.000101892447453022\t0.00020898968160112\t0.00018589786110267\t0.000307514987819811\t0.000357112398084273\t0.000316352014982079\t0.00021198645013364\t0.000691068949900525\t0.000221146831632783\n-B9.266\t4.50617404358542e-05\t7.7187909059995e-06\t1.52411037411529e-05\t1.10253427920853e-05\t4.1745051441984e-05\t3.63488304424524e-05\t3.3290398209022e-05\t1.13169550474572e-05\t9.45184418976979e-06\t7.6012521812347e-06\t6.92482995870393e-06\t3.8268420757911e-05\t2.37195119946984e-06\t2.86004474506151e-05\t3.22860579421692e-06\t2.96039906990133e-06\t2.52808779783966e-05\t0.000142090898957934\t1.10312630129144e-05\t3.60677293639806e-06\t2.97265975382987e-05\t6.66305467846902e-06\t1.14495101906091e-05\n-B9.255\t1.15660880406503e-05\t2.14664012391468e-05\t4.60009639329725e-06\t1.25395676678615e-05\t4.17248489153109e-05\t1.46532714803481e-05\t1.00057270405122e-05\t2.75328532847705e-05\t2.74077840472564e-05\t2.41894891121703e-06\t8.0400281246103e-06\t1.59037103857697e-05\t1.00611731499731e-06\t6.71681516896861e-06\t1.36105357122668e-05\t7.11442411954162e-06\t2.21537557041547e-05\t2.87845824558775e-05\t4.03717597605331e-05\t1.42618582461408e-05\t1.84330229833385e-05\t6.39363012853215e-05\t2.18920831381193e-05\n-B9.246\t2.03293920474837e-07\t2.02423815996018e-05\t4.96598896737477e-06\t1.35705313106542e-05\t3.41075710581766e-05\t6.53017072634504e-05\t4.43984949390479e-06\t1.63183767828055e-05\t2.72484433555238e-06\t8.78724169594538e-06\t8.95623692386308e-07\t2.45735590368271e-05\t5.26105502709834e-06\t2.37539064007069e-05\t2.19035721346259e-05\t1.50517785846819e-05\t2.16082826646081e-05\t2.53649297518041e-05\t1.32773972605395e-05\t1.00977058894297e-05\t1.55783781762885e-05\t3.76630403674761e-05\t2.14582962168246e-05\n-B9.236\t3.37742336734625e-05\t1.09466424044581e-05\t1.26844396116922e-05\t1.41040509503652e-05\t8.32806751647478e-06\t6.89331798338183e-05\t1.31306116922384e-05\t2.44043814312157e-05\t2.60353424850613e-06\t1.5498729364209e-05\t1.12441000124573e-05\t1.90904945628191e-05\t4.77289113406423e-06\t2.6783614160707e-05\t1.81281101162131e-05\t2.27290178082349e-05\t2.2060579242685e-05\t2.02102446881195e-05\t2.82836945109232e-05\t2.6769889759727e-05\t3.20529608453921e-05\t1.46895321061598e-05\t2.72459848898296e-05\n-B9.226\t1.02347475703096e-05\t1.61525191983677e-05\t6.32740402153627e-06\t2.17291460045977e-06\t3.58860102752402e-05\t5.32064617047859e-05\t3.88074184844747e-06\t1.41925328605111e-05\t3.61825110992116e-05\t1.56626397248238e-05\t1.48898939857621e-0'..b'7579\t0.0232263392642444\t0.00538943800528357\t0.00514775819006039\t0.00559553789396426\t0.0173520429506117\t0.028324033261543\n-B0.876\t0.00215863677466562\t0.00369895246404019\t0.00360045348807487\t0.00134769212206423\t0.00218354336599731\t0.00245532683379321\t0.00345022433982449\t0.000717888096909645\t0.00170401747506495\t0.000356847987108017\t0.0041628951177036\t0.005088145578844\t0.00284987245949532\t0.00268286392210182\t0.00197915272339639\t0.0164744229799929\t0.00871859567919084\t0.0291624658349522\t0.00450433606743076\t0.00467317787458834\t0.00464469278467577\t0.0176322957897126\t0.0298903125539951\n-B0.866\t0.00150013418482023\t0.00258508360037412\t0.00238111738536749\t0.000983712268869988\t0.00157378746779101\t0.00184741600638927\t0.00259613706860757\t0.000530590445564721\t0.00114218607490948\t0.000297719443003154\t0.00236377135640083\t0.00299039447289031\t0.00169838032153178\t0.00202478720109677\t0.00155237208983581\t0.00506508824735588\t0.00335278099612616\t0.00916049409218431\t0.00304824370929634\t0.0028945285734165\t0.0028543532645478\t0.00397438831823791\t0.00746021084696681\n-B0.857\t0.000986962374512856\t0.00174301185204418\t0.00155459274530862\t0.00059744100374567\t0.000946611593982685\t0.00119641009019251\t0.00173321235334005\t0.000356899004924163\t0.000758730491964375\t0.000160811437925477\t0.00152510957100737\t0.00196835887814581\t0.00101457930295155\t0.00150335976451684\t0.00101420955937978\t0.0033735623219071\t0.00210956426055451\t0.00493276854725743\t0.00178283936255044\t0.00165275426730159\t0.00170372495712446\t0.00248870525573775\t0.0039846322834038\n-B0.846\t0.000839825601114667\t0.0012769784113784\t0.00110091918664795\t0.000413961172391942\t0.000708888771217311\t0.000778154520699405\t0.00111234240481985\t0.000244663266226838\t0.000484525523691875\t7.68758960306947e-05\t0.000909219126236251\t0.00113056799032888\t0.000631562997579227\t0.00107030332221529\t0.000634580995745331\t0.00106135884542878\t0.000970558123349218\t0.00157698752726719\t0.00109118524592164\t0.0010809000005087\t0.00117405624971632\t0.00104182637112804\t0.00136932315987551\n-B0.836\t0.000540291147081289\t0.00110805916107828\t0.000991944918364915\t0.000259305489167024\t0.000414200683547401\t0.000446851710747917\t0.000739324952553648\t0.00014512091218808\t0.000240131270356258\t1.53279187890163e-05\t0.000995779500719967\t0.00117589795062701\t0.000663607401633198\t0.00072607607121414\t0.000348533637762843\t0.000814771690737036\t0.000852228105038011\t0.00106417265964175\t0.00106436355116083\t0.00088998568772594\t0.00115577335390134\t0.000793475313473202\t0.000969704476916626\n-B0.826\t0.000439210376659004\t0.000622025753244184\t0.0005877341421479\t0.000201776175879904\t0.000325527630159852\t0.000344597178120722\t0.000468730496980652\t0.000169188243600758\t0.000244354283493434\t1.80591932027473e-05\t0.000645393534597378\t0.00076364124043746\t0.000411619698520102\t0.000416731585656504\t0.000256480294202034\t0.000524752271786902\t0.000676304092825243\t0.000814916554483356\t0.000597779964300897\t0.000807012376046873\t0.000712066733726576\t0.000508127245813254\t0.000691958647587166\n-B0.816\t0.000394076959769821\t0.000626251816952311\t0.000644546372165628\t0.000163741793970591\t0.000294493619073591\t0.000396363737760121\t0.000520046367222883\t0.00012853568638618\t0.000243131055493038\t1.18743008584546e-05\t0.000604929046893319\t0.000717510278393041\t0.000373029125568352\t0.000391937364448496\t0.000234261393789731\t0.000523235700797077\t0.000619868853421147\t0.000730622691788109\t0.000640770168804395\t0.000676985988978989\t0.000745527871203007\t0.00061791716531139\t0.000781012740687151\n-B0.806\t0.000336785447055572\t0.000470318285990568\t0.000447571911175899\t0.00015477142985862\t0.000254766661248894\t0.000300355488014835\t0.000386815449880438\t0.000128859420585409\t0.000182934749398549\t1.11417886043334e-05\t0.0003939533156056\t0.000417332638774188\t0.000210616293653824\t0.000296880999894829\t0.000120837576055159\t0.00033047173709954\t0.000388172417071423\t0.000450376987152908\t0.000452051328977898\t0.000485123182275246\t0.00047918667429437\t0.000397128925502763\t0.000516124725384787\n-B0.8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n' |
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diff -r d61f6ceef5d6 -r 475d219739ff test-data/MTBLS1_sampleMetadata.tabular --- a/test-data/MTBLS1_sampleMetadata.tabular Tue Nov 22 05:22:03 2016 -0500 +++ /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 d61f6ceef5d6 -r 475d219739ff test-data/MTBLS1_variableMetadata.tabular --- a/test-data/MTBLS1_variableMetadata.tabular Tue Nov 22 05:22:03 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
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b |
diff -r d61f6ceef5d6 -r 475d219739ff tool_dependencies.xml --- a/tool_dependencies.xml Tue Nov 22 05:22:03 2016 -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-pracma" version="1.8.8"> - <repository changeset_revision="48eb1ff95b33" name="package_r_pracma_1_8_8" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |