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added:
nmr_alignement/.Rhistory nmr_alignement/.shed.yml nmr_alignement/NmrAlignment_script.R nmr_alignement/NmrAlignment_wrapper.R nmr_alignement/NmrAlignment_xml.xml nmr_alignement/static/images/NmrAlignment.png nmr_alignement/test-data/MTBLS1.zip nmr_alignement/test-data/MTBLS1_bucketedData.tabular nmr_alignement/test-data/MTBLS1_sampleMetadata.tabular nmr_alignement/test-data/MTBLS1_variableMetadata.tabular |
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removed:
NmrAlignment_script.R NmrAlignment_wrapper.R NmrAlignment_xml.xml static/images/NmrAlignment.png test-data/MTBLS1.zip test-data/MTBLS1_bucketedData.tabular test-data/MTBLS1_sampleMetadata.tabular test-data/MTBLS1_variableMetadata.tabular |
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| diff -r d690c5ad932f -r 58eecef626da NmrAlignment_script.R --- a/NmrAlignment_script.R Thu Nov 24 12:11:04 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,440 +0,0 @@\n-################################################################################################\n-# NMR SPECTRA ALIGNEMENT USING THE CLUPA ALGORITHM (Vu et al. 2013) #\n-# Included in the speaq package #\n-# User : Galaxy #\n-# Original data : -- #\n-# Starting date : 05-10-2016 #\n-# Version 1 : -- #\n-# #\n-# Input files : datra.frame containing spectra to align #\n-################################################################################################\n-\n-\n-################################################################################################\n-# Bruker files reading #\n-# Input parameters #\n-# - directory: name of your folder containing all experimental samples as sub-directories #\n-# - leftBorder: upper boundary: values greater than this value are not used; #\n-# Default value: 10.0 ppm #\n-# - rightBorder: lower boundary: values lower than this value are not used; #\n-# Default value: 10.0 ppm #\n-# - exclusionZones: spectral regions to exclude (water, solvent or contaminant resonance); #\n-# boolean #\n-# - exclusionZonesBorders: upper and lower boudaries of exclusions zones #\n-# Output parameters #\n-# - truncatedSpectrum_matrice: n x p datamatrix #\n-################################################################################################\n-NmrRead <- function(directory, leftBorder= 10.0, rightBorder= 0.5, exclusionZones=FALSE, exclusionZonesBorders=NULL)\n-{\n- ## Option\n- ##---------------\n- strAsFacL <- options()$stringsAsFactors\n- options(stingsAsFactors=FALSE)\n- options(warn=-1)\n- \n- \n- ## Constants\n- ##---------------\n- topEnvC <- environment()\n- flgC <- "\\n"\n- \n- ## Log file (in case of integration into Galaxy)\n- ##----------------------------------------------\n- # if(!is.null(savLog.txtC))\n- # sink(savLog.txtC, append=TRUE)\n- \n- ## Functions definition\n- ##--------------------- \n- ## RAW BRUKER FILE READING FUNCTION\n- NmRBrucker_read <- function(DataDir,SampleSpectrum)\n- {\n- \n- bruker.get_param <- function (ACQ,paramStr)\n- {\n- regexpStr <- paste("^...",paramStr,"=",sep="")\n- as.numeric(gsub("^[^=]+= ","" ,ACQ[which(simplify2array(regexpr(regexpStr,ACQ))>0)]))\n- }\n- \n- ACQFILE <- "acqus"\n- SPECFILE <- paste(DataDir,"/1r",sep="")\n- PROCFILE <- paste(DataDir,"/procs",sep="")\n- \n- ACQ <- readLines(ACQFILE)\n- TD <- bruker.get_param(ACQ,"TD")\n- SW <- bruker.get_param(ACQ,"SW")\n- SWH <- bruker.get_param(ACQ,"SW_h")\n- DTYPA <- bruker.get_param(ACQ,"DTYPA")\n- BYTORDA <- bruker.get_param(ACQ,"BYTORDA")\n- #ENDIAN=ifelse( BYTORDA==0, "little", "big")\n- ENDIAN <- "little"\n- SIZE=ifelse( DTYPA==0, 4, 8)\n- \n- PROC <- readLines(PROCFILE)\n- OFFSET <- bruker.get_param(PROC,"OFFSET")\n- SI <- bruker.get_param(PROC,"SI")\n- \n- to.read=file(SPECFILE,"rb")\n- maxTDSI=max(TD,SI)\n- # signal<-rev(readBin(to.read, what="int",s'..b'1, maxshift=maxshift, \n- verbose)\n-{\n- ## Peak picking\n- cat("\\n detect peaks....")\n- startTime <- proc.time()\n- peakList <- detectSpecPeaks(X=data, nDivRange=nDivRange, scales=scales, baselineThresh=baselineThresh, \n- SNR.Th = SNR.Th, verbose=verbose)\n- endTime <- proc.time()\n- cat("Peak detection time:",(endTime[3]-startTime[3])/60," minutes")\n-\n- ## Reference spectrum determination\n- if (reference == 0)\n- {\n- cat("\\n Find the spectrum reference...")\n- resFindRef<- findRef(peakList)\n- refInd <- resFindRef$refInd\n- cat("\\n Order of spectrum for reference \\n")\n- for (i in 1:length(resFindRef$orderSpec))\n- {\n- cat(paste(i, ":",resFindRef$orderSpec[i],sep=""), " ")\n- if (i %% 10 == 0) \n- cat("\\n")\n- }\n- cat("\\n The reference is: ", refInd)\n- }\n- else\n- {\n- refInd=reference\n- }\n- ## Spectra alignment to the reference\n- maxshift <- 50\n- Y <- dohCluster(data, peakList=peakList, refInd=refInd, maxShift=maxShift, acceptLostPeak, verbose)\n-\n- ## Output \n- return(Y)\n-}\n-\n-\n-################################################################################################\n-# Principal function #\n-# Input parameters #\n-# - directory: name of your folder containing all experimental samples as sub-directories #\n-# - leftBorder: upper boundary: values greater than this value are not used; #\n-# Default value: 10.0 ppm #\n-# - rightBorder: lower boundary: values lower than this value are not used; #\n-# Default value: 10.0 ppm #\n-# - exclusionZones: spectral regions to exclude (water, solvent or contaminant resonance); #\n-# boolean #\n-# - exclusionZonesBorders: upper and lower boudaries of exclusions zones #\n-# - verbose: printing out process information (boolean) #\n-# - reference: reference spectrum number, if exists #\n-# Default value: 0 (automatic detection #\n-# - nDivRange: size of a single small segment after division of the whole spectrum #\n-# Default value: 64 #\n-# - baselineThresh: removal of all the peaks with intensity lower than this threshold #\n-# Default value: 50000 #\n-# Output parameters: list containing #\n-# - data.read: n x p matrix #\n-# - data.aligned: n x p matrix #\n-################################################################################################\n-nmr.alignment <- function(directory, leftBorder= 10.0, rightBorder= 0.5, exclusionZones=FALSE, \n- exclusionZonesBorders=NULL, reference=0, nDivRange=64, baselineThresh=50000, maxshift=50, verbose=FALSE)\n-{\n- data.read <- NmrRead(directory=directory, leftBorder=leftBorder, rightBorder=rightBorder, exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders)\n- rownames(data.read) <- data.read[,1]\n- data.read <- data.read[,-1]\n- data.read <- t(data.read)\n- data.aligned <- cluPA.alignment(data=data.read, reference=reference, nDivRange=nDivRange, \n- baselineThresh=baselineThresh, maxshift=maxshift, verbose=verbose)\n-\n- return(list(data.read,data.aligned))\n-}\n-\n' |
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| diff -r d690c5ad932f -r 58eecef626da NmrAlignment_wrapper.R --- a/NmrAlignment_wrapper.R Thu Nov 24 12:11:04 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,176 +0,0 @@ -#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file - -## 06102016_NmrAlignment_wrapper.R -## Marie Tremblay-Franco -## marie.tremblay-franco@toulouse.inra.fr - -runExampleL <- FALSE - -##------------------------------ -## Options -##------------------------------ -strAsFacL <- options()$stringsAsFactors -options(stringsAsFactors = FALSE) - - -##------------------------------ -## Libraries loading -##------------------------------ - # ParseCommandArgs function -library(batch) - # Alignment -library(speaq) - - -# R script call -source_local <- function(fname) -{ - argv <- commandArgs(trailingOnly = FALSE) - base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) - source(paste(base_dir, fname, sep="/")) -} -# Function import -source_local("NmrAlignment_script.R") - - -##------------------------------ -## Errors ????????????????????? -##------------------------------ - - -##------------------------------ -## Constants -##------------------------------ -topEnvC <- environment() -flagC <- "\n" - - -##------------------------------ -## Script -##------------------------------ -if(!runExampleL) - argLs <- parseCommandArgs(evaluate=FALSE) - - -## Parameters Loading -##------------------- - # Inputs - ## Library of spectra to align -if (!is.null(argLs[["zipfile"]])){ - zipfile= argLs[["zipfile"]] - directory=unzip(zipfile, list=F) - directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") -} else if (!is.null(argLs[["library"]])){ - directory=argLs[["library"]] - if(!file.exists(directory)){ - error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.") - print(error_message) - stop(error_message) - } -} - - - ## Spectral width -leftBorder <- argLs[["left_border"]] -rightBorder <- argLs[["right_border"]] - - ##Exclusion zone(s) -exclusionZones <- argLs[["zone_exclusion_choices.choice"]] -exclusionZonesBorders <- NULL -if (!is.null(argLs$zone_exclusion_left)) -{ - for(i in which(names(argLs)=="zone_exclusion_left")) - { - exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) - } -} - - ## Reference spectrum -reference <- argLs[["reference"]] - - ## Size of a small nDivRange -nDivRange <- argLs[["nDivRange"]] - - ## Intensity threshold for peak removal -baselineThresh <- argLs[["baselineThresh"]] - - - # Outputs -logOut <- argLs[["logOut"]] -alignedSpectra <- argLs[["alignedSpectra"]] -graphOut <- argLs[["graphOut"]] - - -## Checking arguments -##------------------- -error.stock <- "\n" -if(length(error.stock) > 1) - stop(error.stock) - - -## Computation -##------------ -directory.alignement <- nmr.alignment(directory=directory,leftBorder=leftBorder,rightBorder=rightBorder,exclusionZones=exclusionZones, - exclusionZonesBorders=exclusionZonesBorders, reference=reference, nDivRange=nDivRange, - baselineThresh=baselineThresh, maxshift=50, verbose=FALSE) -directory.raw <- directory.alignement[[1]] -directory.aligned <- directory.alignement[[2]] - -## Saving -##------- - # Aligned spectra -t.directory.aligned <- t(directory.aligned) -rownames(t.directory.aligned) <- colnames(directory.aligned) -# colnames(t.directory.aligned) <- c("Bucket",colnames(t.directory.aligned)) -write.table(t.directory.aligned,file=alignedSpectra,row.names=TRUE,quote=FALSE,sep="\t") - - -excludedZone <- NULL -for (c in 1:length(exclusionZonesBorders)) -{ - excludedZone <- c(excludedZone,exclusionZonesBorders[[c]]) - excludedZone <- sort(excludedZone) -} - -## Graphical output: overlay of raw and estimated spectra -pdf(graphOut,onefile=TRUE) -par(mfrow=c(2,1)) - -raw.spectra <- data.frame(directory.raw) -colnames(raw.spectra) <- substr(colnames(raw.spectra),2,7) - -aligned.spectra <- data.frame(directory.aligned) -colnames(aligned.spectra) <- substr(colnames(aligned.spectra),2,7) - -drawSpec(raw.spectra,xlab="", ylab="Raw spectra", main="") -drawSpec(aligned.spectra,xlab="", ylab="Aligned spectra", main="") - -nbZones <- length(excludedZone)/2 -if (nbZones != 0) -{ - n <- length(excludedZone) - drawSpec(raw.spectra[,1:which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n])[1]],xlab="", ylab="Raw spectra", main="") - drawSpec(aligned.spectra[,1:which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n])[1]],xlab="", ylab="Aligned spectra", main="") - - n <- n - 1 - while (n >= nbZones & nbZones > 1) - { - drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n])[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n-1])[1])],xlab="", ylab="Raw spectra", main="") - drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n])[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n-1])[1])],xlab="", ylab="Aligned spectra", main="") - n <- n - 2 - } - - drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[1])[1]):ncol(raw.spectra)],xlab="", ylab="Raw spectra", main="") - drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[1])[1]):ncol(aligned.spectra)],xlab="", ylab="Aligned spectra", main="") -} -drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == 2.4)[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == 2.8)[1])],xlab="", ylab="Raw spectra", main="") -drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == 2.4)[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == 2.8)[1])],xlab="", ylab="Aligned spectra", main="") - -dev.off() - - -## Ending -##--------------------- -cat("\nEnd of 'NMR alignment' Galaxy module call: ", as.character(Sys.time()), sep = "") -options(stringsAsFactors = strAsFacL) -rm(list = ls()) |
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| diff -r d690c5ad932f -r 58eecef626da NmrAlignment_xml.xml --- a/NmrAlignment_xml.xml Thu Nov 24 12:11:04 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,258 +0,0 @@\n-<tool id="NmrAlignment" name="NMR_Alignment" version="2016-10-07">\n-\n-\t <description> Alignment of NMR spectra based on the Cluster-based Peak Alignment (CluPA) algorithm </description>\n-\n-\t <requirements>\n- <requirement type="package" version="3.1.2">R</requirement>\n-\t <requirement type="package" version="1.1_4">r-batch</requirement>\n-\t <requirement type="package" version="1.2.1">r-speaq</requirement>\n- \t</requirements>\n-\n- <stdio>\n- <exit_code range="1:" level="fatal" />\n- </stdio>\n-\n- \t<command>\n-\t\t## Wrapper\n- Rscript $__tool_directory__/NmrAlignment_wrapper.R\n-\n-\t\t## File input\n- #if $inputs.input == "lib":\n- library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library\n- #elif $inputs.input == "zip_file":\n- zipfile $inputs.zip_file\n- #end if\n-\n-\t\t## Spectra borders\n-\t\tleft_border $left_border\n-\t\tright_border $right_border\n-\n-\n-\t\t## Exclusion zone\n-\t\tzone_exclusion_choices.choice ${zone_exclusion_choices.choice}\n-\t\t#if str($zone_exclusion_choices.choice) == \'yes\':\n-\t\t\t#for $i in $zone_exclusion_choices.conditions:\n-\t\t\t\tzone_exclusion_left ${i.zone_exclusion_left}\n-\t\t\t\tzone_exclusion_right ${i.zone_exclusion_right}\n-\t\t\t#end for\n-\t\t#end if\n-\n-\t\t## Reference spectrum\n-\t\treference $reference\n-\n-\t\t## Segment size\n-\t\tnDivRange $nDivRange\n-\n-\t\t## Intensity threshold\n-\t\tbaselineThresh $baselineThresh\n-\n-\t\t## Outputs\n-\t\tlogOut $logOut\n-\t\talignedSpectra $alignedSpectra\n-\t\tgraphOut $graphOut\n-\t </command>\n-\n- \t<inputs>\n- <conditional name="inputs">\n- <param name="input" type="select" label="Choose your inputs method" >\n- <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>\n- <option value="lib" >Library directory name</option>\n- </param>\n- <when value="zip_file">\n- <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />\n- </when>\n- <when value="lib">\n- <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >\n- <validator type="empty_field"/>\n- </param>\n- </when>\n- </conditional>\n-\n-\t\t<param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>\n-\t\t<param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>\n-\n-\t\t<conditional name="zone_exclusion_choices">\n-\t\t\t<param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >\n-\t\t\t\t<option value="yes" > yes </option>\n-\t\t\t\t<option value="no" selected="true"> no </option>\n-\t\t\t</param>\n-\t\t\t<when value="yes">\n-\t\t\t\t<repeat name="conditions" title="exclusion zones">\n-\t\t\t\t\t<param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />\n-\t\t\t\t\t<param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />\n-\t\t\t\t</repeat>\n-\t\t\t</when>\n- <when value="no" />\n-\t\t</conditional>\n-\n-\t\t<param name="reference" type="integer" value="0" help="Number of the reference spectrum. Default value is 0: automatic determination of the reference spectrum" />\n-\n-\t\t<param name="nDivRange" type="integer" value="64" help="Size of a single small segment after division of spectra. Default value is 64" />\n-\n-\t\t<param name="baselineThresh" type="integer" value="1" help="Threshold to remove all peaks with intensity lower this value. Default value is 1" />\n-\n-\t</inputs>\n-\n-\t<outputs>\n-\t\t<data format="txt" name="logOut" label="${tool.name}_log" />\n-\t\t<data format="tabular" name="alignedSpectra" label="${tool.name}_alignedSpectra" />\n-\t\t<data format="pdf" name="graphOut" label="${tool.name}_graph" />\n-\t</outputs>\n-\n-\t<help>\n-\n-.. class:: infomark\n-\n-**'..b'------------\n-\n-**Upstream tools**\n-\n-========================= ================= =======\n-Name output file format\n-========================= ================= =======\n-NA NA NA\n-========================= ================= =======\n-\n-\n-**Downstream tools**\n-\n-+---------------------------+----------------------+--------+\n-| Name | Output file | Format |\n-+===========================+======================+========+\n-|NmrBucketing | dataMatrix.tsv | Tabular|\n-+---------------------------+----------------------+--------+\n-| | sampleMetadata.tsv | Tabular|\n-+---------------------------+----------------------+--------+\n-| | variableMetadata.tsv | Tabular|\n-+---------------------------+----------------------+--------+\n-|NmrNormalization | dataMatrix.tsv | Tabular|\n-+---------------------------+----------------------+--------+\n-| | sampleMetadata.tsv | Tabular|\n-+---------------------------+----------------------+--------+\n-| | variableMetadata.tsv | Tabular|\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-| 1 : Choose your inputs | zip |\n-+---------------------------+------------+\n-\n-**Choose your inputs**\n-\n- | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).\n-\n-\n-----------\n-Parameters\n-----------\n-\n-Bucket width\n-\t| size of windows\n-\t|\n-\n-Left limit\n-\t| Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm\n-\t|\n-\n-Right limit\n-\t| Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm\n-\t|\n-\n-Exclusion zone(s)\n-\t| Spectral regions to exclude, water, solvents, ... resonance\n-\t| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,\n-\t| If NO: no zone to exclude\n-\t| Default value is NO\n-\t|\n-\n-Left exclusion zone\n-\t| Upper boundary of exclusion zone\n-\t|\n-\n-Right exclusion zone\n-\t| Lower boundary of exclusion zone\n-\n-| *Notes:*\n-| - these parameters can be used several times using the "Add new exclusion zones" button\n-|\n-\n-Reference spectrum\n-\t| spectrum to which other spectra are aligned\n-\t| Default value is 0: heuristic strategy to find the optimal template developped in the speaq package\n-\t|\n-\n-Segment size\n-\t| Size of a single small segment after division of spectra\n-\t| Default value: 64 (minimal value adviced)\n-\t|\n-\n-Intensity threshold\n-\t| All peaks with an intensity below this threshold are removed\n-\t| Default value: 1\n-\t|\n-\n-\n-------------\n-Output files\n-------------\n-\n-alignedSpectra.tsv\n-\t| tabular output\n-\t| Data matrix with p rows (ppm) and n columns (samples) containing the aligned intensities\n-\t|\n-\n-graphOut.pdf\n-\t| pdf output\n-\t| Graphical chart of raw and aligned data: whole spectral width, "zoomed" zones depending on the exclusion zones, spectral zone between 2.8 and 2.4ppm corresponding to the citric acid\n-\n-\n----------------------------------------------------\n-\n----------------\n-Example\n----------------\n-\n-\n-.. image:: ./static/images/NmrAlignment.png\n- :width: 500\n-\n- </help>\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btu813</citation>\n- </citations>\n-\n-</tool>\n' |
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| diff -r d690c5ad932f -r 58eecef626da nmr_alignement/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/.shed.yml Thu Mar 02 10:23:37 2017 -0500 |
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| @@ -0,0 +1,7 @@ +categories: [Metabolomics] +description: '[Metabolomics][W4M][NMR] NMR Alignment - Alignment of NMR spectra based on the Cluster-based Peak Alignment (CluPA) algorithm' +homepage_url: http://workflow4metabolomics.org +long_description: 'Part of the W4M project: http://workflow4metabolomics.org' +name: nmr_alignment +owner: marie-tremblay-metatoul +remote_repository_url: https://github.com/workflow4metabolomics/nmr_alignment |
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| diff -r d690c5ad932f -r 58eecef626da nmr_alignement/NmrAlignment_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/NmrAlignment_script.R Thu Mar 02 10:23:37 2017 -0500 |
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| b'@@ -0,0 +1,440 @@\n+################################################################################################\r\n+# NMR SPECTRA ALIGNEMENT USING THE CLUPA ALGORITHM (Vu et al. 2013) #\r\n+# Included in the speaq package #\r\n+# User : Galaxy #\r\n+# Original data : -- #\r\n+# Starting date : 05-10-2016 #\r\n+# Version 1 : -- #\r\n+# #\r\n+# Input files : datra.frame containing spectra to align #\r\n+################################################################################################\r\n+\r\n+\r\n+################################################################################################\r\n+# Bruker files reading #\r\n+# Input parameters #\r\n+# - directory: name of your folder containing all experimental samples as sub-directories #\r\n+# - leftBorder: upper boundary: values greater than this value are not used; #\r\n+# Default value: 10.0 ppm #\r\n+# - rightBorder: lower boundary: values lower than this value are not used; #\r\n+# Default value: 10.0 ppm #\r\n+# - exclusionZones: spectral regions to exclude (water, solvent or contaminant resonance); #\r\n+# boolean #\r\n+# - exclusionZonesBorders: upper and lower boudaries of exclusions zones #\r\n+# Output parameters #\r\n+# - truncatedSpectrum_matrice: n x p datamatrix #\r\n+################################################################################################\r\n+NmrRead <- function(directory, leftBorder= 10.0, rightBorder= 0.5, exclusionZones=FALSE, exclusionZonesBorders=NULL)\r\n+{\r\n+ ## Option\r\n+ ##---------------\r\n+ strAsFacL <- options()$stringsAsFactors\r\n+ options(stingsAsFactors=FALSE)\r\n+ options(warn=-1)\r\n+ \r\n+ \r\n+ ## Constants\r\n+ ##---------------\r\n+ topEnvC <- environment()\r\n+ flgC <- "\\n"\r\n+ \r\n+ ## Log file (in case of integration into Galaxy)\r\n+ ##----------------------------------------------\r\n+ # if(!is.null(savLog.txtC))\r\n+ # sink(savLog.txtC, append=TRUE)\r\n+ \r\n+ ## Functions definition\r\n+ ##--------------------- \r\n+ ## RAW BRUKER FILE READING FUNCTION\r\n+ NmRBrucker_read <- function(DataDir,SampleSpectrum)\r\n+ {\r\n+ \r\n+ bruker.get_param <- function (ACQ,paramStr)\r\n+ {\r\n+ regexpStr <- paste("^...",paramStr,"=",sep="")\r\n+ as.numeric(gsub("^[^=]+= ","" ,ACQ[which(simplify2array(regexpr(regexpStr,ACQ))>0)]))\r\n+ }\r\n+ \r\n+ ACQFILE <- "acqus"\r\n+ SPECFILE <- paste(DataDir,"/1r",sep="")\r\n+ PROCFILE <- paste(DataDir,"/procs",sep="")\r\n+ \r\n+ ACQ <- readLines(ACQFILE)\r\n+ TD <- bruker.get_param(ACQ,"TD")\r\n+ SW <- bruker.get_param(ACQ,"SW")\r\n+ SWH <- bruker.get_param(ACQ,"SW_h")\r\n+ DTYPA <- bruker.get_param(ACQ,"DTYPA")\r\n+ BYTORDA <- bruker.get_param(ACQ,"BYTORDA")\r\n+ #ENDIAN=ifelse( BYTORDA==0, "little", "big")\r\n+ ENDIAN <- "little"\r\n+ SIZE=ifelse( DTYPA==0, 4, 8)\r\n+ \r\n+ PROC <- readLines(PROCFILE)\r\n+ OFFSET <- bruker.get_param(PROC,"OFFSET")\r\n+ SI <- bruker.get_param(PROC,"SI")\r\n+ \r\n+ to.read=file(SPECFILE,"rb"'..b'eak picking\r\n+ cat("\\n detect peaks....")\r\n+ startTime <- proc.time()\r\n+ peakList <- detectSpecPeaks(X=data, nDivRange=nDivRange, scales=scales, baselineThresh=baselineThresh, \r\n+ SNR.Th = SNR.Th, verbose=verbose)\r\n+ endTime <- proc.time()\r\n+ cat("Peak detection time:",(endTime[3]-startTime[3])/60," minutes")\r\n+\r\n+ ## Reference spectrum determination\r\n+ if (reference == 0)\r\n+ {\r\n+ cat("\\n Find the spectrum reference...")\r\n+ resFindRef<- findRef(peakList)\r\n+ refInd <- resFindRef$refInd\r\n+ cat("\\n Order of spectrum for reference \\n")\r\n+ for (i in 1:length(resFindRef$orderSpec))\r\n+ {\r\n+ cat(paste(i, ":",resFindRef$orderSpec[i],sep=""), " ")\r\n+ if (i %% 10 == 0) \r\n+ cat("\\n")\r\n+ }\r\n+ cat("\\n The reference is: ", refInd)\r\n+ }\r\n+ else\r\n+ {\r\n+ refInd=reference\r\n+ }\r\n+ ## Spectra alignment to the reference\r\n+ maxshift <- 50\r\n+ Y <- dohCluster(data, peakList=peakList, refInd=refInd, maxShift=maxShift, acceptLostPeak, verbose)\r\n+\r\n+ ## Output \r\n+ return(Y)\r\n+}\r\n+\r\n+\r\n+################################################################################################\r\n+# Principal function #\r\n+# Input parameters #\r\n+# - directory: name of your folder containing all experimental samples as sub-directories #\r\n+# - leftBorder: upper boundary: values greater than this value are not used; #\r\n+# Default value: 10.0 ppm #\r\n+# - rightBorder: lower boundary: values lower than this value are not used; #\r\n+# Default value: 10.0 ppm #\r\n+# - exclusionZones: spectral regions to exclude (water, solvent or contaminant resonance); #\r\n+# boolean #\r\n+# - exclusionZonesBorders: upper and lower boudaries of exclusions zones #\r\n+# - verbose: printing out process information (boolean) #\r\n+# - reference: reference spectrum number, if exists #\r\n+# Default value: 0 (automatic detection #\r\n+# - nDivRange: size of a single small segment after division of the whole spectrum #\r\n+# Default value: 64 #\r\n+# - baselineThresh: removal of all the peaks with intensity lower than this threshold #\r\n+# Default value: 50000 #\r\n+# Output parameters: list containing #\r\n+# - data.read: n x p matrix #\r\n+# - data.aligned: n x p matrix #\r\n+################################################################################################\r\n+nmr.alignment <- function(directory, leftBorder= 10.0, rightBorder= 0.5, exclusionZones=FALSE, \r\n+ exclusionZonesBorders=NULL, reference=0, nDivRange=64, baselineThresh=50000, maxshift=50, verbose=FALSE)\r\n+{\r\n+ data.read <- NmrRead(directory=directory, leftBorder=leftBorder, rightBorder=rightBorder, exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders)\r\n+ rownames(data.read) <- data.read[,1]\r\n+ data.read <- data.read[,-1]\r\n+ data.read <- t(data.read)\r\n+ data.aligned <- cluPA.alignment(data=data.read, reference=reference, nDivRange=nDivRange, \r\n+ baselineThresh=baselineThresh, maxshift=maxshift, verbose=verbose)\r\n+\r\n+ return(list(data.read,data.aligned))\r\n+}\r\n+\r\n' |
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| diff -r d690c5ad932f -r 58eecef626da nmr_alignement/NmrAlignment_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/NmrAlignment_wrapper.R Thu Mar 02 10:23:37 2017 -0500 |
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| @@ -0,0 +1,176 @@ +#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file + +## 06102016_NmrAlignment_wrapper.R +## Marie Tremblay-Franco +## marie.tremblay-franco@toulouse.inra.fr + +runExampleL <- FALSE + +##------------------------------ +## Options +##------------------------------ +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + + +##------------------------------ +## Libraries loading +##------------------------------ + # ParseCommandArgs function +library(batch) + # Alignment +library(speaq) + + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} +# Function import +source_local("NmrAlignment_script.R") + + +##------------------------------ +## Errors ????????????????????? +##------------------------------ + + +##------------------------------ +## Constants +##------------------------------ +topEnvC <- environment() +flagC <- "\n" + + +##------------------------------ +## Script +##------------------------------ +if(!runExampleL) + argLs <- parseCommandArgs(evaluate=FALSE) + + +## Parameters Loading +##------------------- + # Inputs + ## Library of spectra to align +if (!is.null(argLs[["zipfile"]])){ + zipfile= argLs[["zipfile"]] + directory=unzip(zipfile, list=F) + directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") +} else if (!is.null(argLs[["library"]])){ + directory=argLs[["library"]] + if(!file.exists(directory)){ + error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.") + print(error_message) + stop(error_message) + } +} + + + ## Spectral width +leftBorder <- argLs[["left_border"]] +rightBorder <- argLs[["right_border"]] + + ##Exclusion zone(s) +exclusionZones <- argLs[["zone_exclusion_choices.choice"]] +exclusionZonesBorders <- NULL +if (!is.null(argLs$zone_exclusion_left)) +{ + for(i in which(names(argLs)=="zone_exclusion_left")) + { + exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) + } +} + + ## Reference spectrum +reference <- argLs[["reference"]] + + ## Size of a small nDivRange +nDivRange <- argLs[["nDivRange"]] + + ## Intensity threshold for peak removal +baselineThresh <- argLs[["baselineThresh"]] + + + # Outputs +logOut <- argLs[["logOut"]] +alignedSpectra <- argLs[["alignedSpectra"]] +graphOut <- argLs[["graphOut"]] + + +## Checking arguments +##------------------- +error.stock <- "\n" +if(length(error.stock) > 1) + stop(error.stock) + + +## Computation +##------------ +directory.alignement <- nmr.alignment(directory=directory,leftBorder=leftBorder,rightBorder=rightBorder,exclusionZones=exclusionZones, + exclusionZonesBorders=exclusionZonesBorders, reference=reference, nDivRange=nDivRange, + baselineThresh=baselineThresh, maxshift=50, verbose=FALSE) +directory.raw <- directory.alignement[[1]] +directory.aligned <- directory.alignement[[2]] + +## Saving +##------- + # Aligned spectra +t.directory.aligned <- t(directory.aligned) +rownames(t.directory.aligned) <- colnames(directory.aligned) +# colnames(t.directory.aligned) <- c("Bucket",colnames(t.directory.aligned)) +write.table(t.directory.aligned,file=alignedSpectra,row.names=TRUE,quote=FALSE,sep="\t") + + +excludedZone <- NULL +for (c in 1:length(exclusionZonesBorders)) +{ + excludedZone <- c(excludedZone,exclusionZonesBorders[[c]]) + excludedZone <- sort(excludedZone) +} + +## Graphical output: overlay of raw and estimated spectra +pdf(graphOut,onefile=TRUE) +par(mfrow=c(2,1)) + +raw.spectra <- data.frame(directory.raw) +colnames(raw.spectra) <- substr(colnames(raw.spectra),2,7) + +aligned.spectra <- data.frame(directory.aligned) +colnames(aligned.spectra) <- substr(colnames(aligned.spectra),2,7) + +drawSpec(raw.spectra,xlab="", ylab="Raw spectra", main="") +drawSpec(aligned.spectra,xlab="", ylab="Aligned spectra", main="") + +nbZones <- length(excludedZone)/2 +if (nbZones != 0) +{ + n <- length(excludedZone) + drawSpec(raw.spectra[,1:which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n])[1]],xlab="", ylab="Raw spectra", main="") + drawSpec(aligned.spectra[,1:which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n])[1]],xlab="", ylab="Aligned spectra", main="") + + n <- n - 1 + while (n >= nbZones & nbZones > 1) + { + drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n])[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n-1])[1])],xlab="", ylab="Raw spectra", main="") + drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n])[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n-1])[1])],xlab="", ylab="Aligned spectra", main="") + n <- n - 2 + } + + drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[1])[1]):ncol(raw.spectra)],xlab="", ylab="Raw spectra", main="") + drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[1])[1]):ncol(aligned.spectra)],xlab="", ylab="Aligned spectra", main="") +} +drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == 2.4)[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == 2.8)[1])],xlab="", ylab="Raw spectra", main="") +drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == 2.4)[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == 2.8)[1])],xlab="", ylab="Aligned spectra", main="") + +dev.off() + + +## Ending +##--------------------- +cat("\nEnd of 'NMR alignment' Galaxy module call: ", as.character(Sys.time()), sep = "") +options(stringsAsFactors = strAsFacL) +rm(list = ls()) |
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| diff -r d690c5ad932f -r 58eecef626da nmr_alignement/NmrAlignment_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/NmrAlignment_xml.xml Thu Mar 02 10:23:37 2017 -0500 |
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| b'@@ -0,0 +1,247 @@\n+<tool id="NmrAlignment" name="NMR spectra alignment" version="2.0.1">\r\n+\t<description>based on the Cluster-based Peak Alignment (CluPA) algorithm</description>\r\n+\t <requirements>\r\n+ <requirement type="package" version="3.1.2">R</requirement>\r\n+\t <requirement type="package" version="1.1_4">r-batch</requirement>\r\n+\t <requirement type="package" version="1.2.1">r-speaq</requirement>\r\n+ \t</requirements>\r\n+ <stdio>\r\n+ <exit_code range="1:" level="fatal" />\r\n+ </stdio>\r\n+ \t<command>\r\n+\t\t## Wrapper\r\n+ Rscript \'$__tool_directory__/NmrAlignment_wrapper.R\'\r\n+\r\n+\t\t## File input\r\n+ #if $inputs.input == "lib":\r\n+ library \'$__app__.config.user_library_import_dir/$__user_email__/$inputs.library\'\r\n+ #elif $inputs.input == "zip_file":\r\n+ zipfile \'$inputs.zip_file\'\r\n+ #end if\r\n+\r\n+\t\t## Spectra borders\r\n+\t\tleft_border $left_border\r\n+\t\tright_border $right_border\r\n+\r\n+\t\t## Exclusion zone\r\n+\t\tzone_exclusion_choices.choice ${zone_exclusion_choices.choice}\r\n+\t\t#if str($zone_exclusion_choices.choice) == \'yes\':\r\n+\t\t\t#for $i in $zone_exclusion_choices.conditions:\r\n+\t\t\t\tzone_exclusion_left ${i.zone_exclusion_left}\r\n+\t\t\t\tzone_exclusion_right ${i.zone_exclusion_right}\r\n+\t\t\t#end for\r\n+\t\t#end if\r\n+\r\n+\t\t## Reference spectrum\r\n+\t\treference $reference\r\n+\r\n+\t\t## Segment size\r\n+\t\tnDivRange $nDivRange\r\n+\r\n+\t\t## Intensity threshold\r\n+\t\tbaselineThresh $baselineThresh\r\n+\r\n+\t\t## Outputs\r\n+\t\tlogOut \'$logOut\'\r\n+\t\talignedSpectra \'$alignedSpectra\'\r\n+\t\tgraphOut \'$graphOut\'\r\n+\t</command>\r\n+ \t<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="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="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+ </conditional>\r\n+\r\n+\t\t<param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>\r\n+\t\t<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+\t\t<conditional name="zone_exclusion_choices">\r\n+\t\t\t<param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >\r\n+\t\t\t\t<option value="yes" > yes </option>\r\n+\t\t\t\t<option value="no" selected="true"> no </option>\r\n+\t\t\t</param>\r\n+\t\t\t<when value="yes">\r\n+\t\t\t\t<repeat name="conditions" title="exclusion zones">\r\n+\t\t\t\t\t<param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />\r\n+\t\t\t\t\t<param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />\r\n+\t\t\t\t</repeat>\r\n+\t\t\t</when>\r\n+ <when value="no" />\r\n+\t\t</conditional>\r\n+\t\t<param name="reference" type="integer" value="0" help="Number of the reference spectrum. Default value is 0: automatic determination of the reference spectrum" />\r\n+\t\t<param name="nDivRange" type="integer" value="64" help="Size of a single small segment after division of spectra. Default value is 64" />\r\n+\t\t<param name="baselineThresh" type="integer" value="1" help="Threshold to remove all peaks with intensity lower this value. Default value is 1" />\r\n+\t</inputs>\r\n+\r\n+\t<outputs>\r\n+\t\t<data format="txt" name="logOut" label="${tool.name}_log" />\r\n+\t\t<data format="tabular" name="alignedSpectra" label="${tool.name}_alignedSpectra" />\r\n+\t\t<data format="pdf" name="graphOut" label="${tool.name}_graph" />\r'..b' file format\r\n+========================= ================= =======\r\n+NA NA NA\r\n+========================= ================= =======\r\n+\r\n+\r\n+**Downstream tools**\r\n+\r\n++---------------------------+----------------------+--------+\r\n+| Name | Output file | Format |\r\n++===========================+======================+========+\r\n+|NmrBucketing | dataMatrix.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+| | sampleMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+| | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+|NmrNormalization | dataMatrix.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+| | sampleMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+| | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+|Univariate | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+|Multivariate | sampleMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+| | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+\r\n+\r\n+-----------\r\n+Input files\r\n+-----------\r\n+\r\n++---------------------------+------------+\r\n+| Parameter : num + label | Format |\r\n++===========================+============+\r\n+| 1 : Choose your inputs | zip |\r\n++---------------------------+------------+\r\n+\r\n+**Choose your inputs**\r\n+\r\n+ | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).\r\n+\r\n+\r\n+----------\r\n+Parameters\r\n+----------\r\n+\r\n+Bucket width\r\n+\t| size of windows\r\n+\t|\r\n+\r\n+Left limit\r\n+\t| Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm\r\n+\t|\r\n+\r\n+Right limit\r\n+\t| Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm\r\n+\t|\r\n+\r\n+Exclusion zone(s)\r\n+\t| Spectral regions to exclude, water, solvents, ... resonance\r\n+\t| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,\r\n+\t| If NO: no zone to exclude\r\n+\t| Default value is NO\r\n+\t|\r\n+\r\n+Left exclusion zone\r\n+\t| Upper boundary of exclusion zone\r\n+\t|\r\n+\r\n+Right exclusion zone\r\n+\t| 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+Reference spectrum\r\n+\t| spectrum to which other spectra are aligned\r\n+\t| Default value is 0: heuristic strategy to find the optimal template developped in the speaq package\r\n+\t|\r\n+\r\n+Segment size\r\n+\t| Size of a single small segment after division of spectra\r\n+\t| Default value: 64 (minimal value adviced)\r\n+\t|\r\n+\r\n+Intensity threshold\r\n+\t| All peaks with an intensity below this threshold are removed\r\n+\t| Default value: 1\r\n+\t|\r\n+\r\n+\r\n+------------\r\n+Output files\r\n+------------\r\n+\r\n+alignedSpectra.tsv\r\n+\t| tabular output\r\n+\t| Data matrix with p rows (ppm) and n columns (samples) containing the aligned intensities\r\n+\t|\r\n+\r\n+graphOut.pdf\r\n+\t| pdf output\r\n+\t| Graphical chart of raw and aligned data: whole spectral width, "zoomed" zones depending on the exclusion zones, spectral zone between 2.8 and 2.4ppm corresponding to the citric acid\r\n+\r\n+\r\n+---------------------------------------------------\r\n+\r\n+---------------\r\n+Example\r\n+---------------\r\n+\r\n+\r\n+.. image:: ./static/images/NmrAlignment.png\r\n+ :width: 500\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 d690c5ad932f -r 58eecef626da nmr_alignement/test-data/MTBLS1.zip |
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| diff -r d690c5ad932f -r 58eecef626da nmr_alignement/test-data/MTBLS1_bucketedData.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/test-data/MTBLS1_bucketedData.tabular Thu Mar 02 10:23:37 2017 -0500 |
| b |
| b'@@ -0,0 +1,595 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|
| b |
| diff -r d690c5ad932f -r 58eecef626da nmr_alignement/test-data/MTBLS1_sampleMetadata.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/test-data/MTBLS1_sampleMetadata.tabular Thu Mar 02 10:23:37 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 d690c5ad932f -r 58eecef626da nmr_alignement/test-data/MTBLS1_variableMetadata.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/test-data/MTBLS1_variableMetadata.tabular Thu Mar 02 10:23:37 2017 -0500 |
| b |
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| diff -r d690c5ad932f -r 58eecef626da static/images/NmrAlignment.png |
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| Binary file static/images/NmrAlignment.png has changed |
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| diff -r d690c5ad932f -r 58eecef626da test-data/MTBLS1.zip |
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| Binary file test-data/MTBLS1.zip has changed |
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| diff -r d690c5ad932f -r 58eecef626da test-data/MTBLS1_bucketedData.tabular --- a/test-data/MTBLS1_bucketedData.tabular Thu Nov 24 12:11:04 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,595 +0,0 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|
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| diff -r d690c5ad932f -r 58eecef626da test-data/MTBLS1_sampleMetadata.tabular --- a/test-data/MTBLS1_sampleMetadata.tabular Thu Nov 24 12:11:04 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 d690c5ad932f -r 58eecef626da test-data/MTBLS1_variableMetadata.tabular --- a/test-data/MTBLS1_variableMetadata.tabular Thu Nov 24 12:11:04 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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