# HG changeset patch
# User marie-tremblay-metatoul
# Date 1517308630 18000
# Node ID a8e85c07dc7b50a2bdc12e3922750ca5c2c89282
Uploaded
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/.shed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation/.shed Tue Jan 30 05:37:10 2018 -0500
@@ -0,0 +1,7 @@
+categories: [Metabolomics]
+description: '[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation'
+homepage_url: http://workflow4metabolomics.org
+long_description: 'Part of the W4M project: http://workflow4metabolomics.org'
+name: nmr_annotation
+owner: marie-tremblay-metatoul
+remote_repository_url: https://github.com/workflow4metabolomics/nmr_annotation
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/DrawSpec.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation/DrawSpec.R Tue Jan 30 05:37:10 2018 -0500
@@ -0,0 +1,74 @@
+drawSpec <- function (X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1,
+ xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0)
+{
+ groupLabel_name = groupLabel
+ X = as.data.frame(X)
+# colnames(X) = c(1:ncol(X))
+ X = as.matrix(X)
+ if (highBound != -1) {
+ for (i in 1:nrow(X)) {
+ myIndex = which(X[i, ] > highBound)
+ X[i, myIndex] = highBound
+ }
+ }
+ if (lowBound != -1) {
+ for (i in 1:nrow(X)) {
+ myIndex = which(X[i, ] < lowBound)
+ X[i, myIndex] = lowBound
+ }
+ }
+ if (is.null(groupLabel)) {
+ groupLabel = c(1:nrow(X))
+ groupLabel = as.factor(groupLabel)
+ }
+ else {
+ levels(groupLabel) = c(1:length(levels(groupLabel)))
+ }
+ if (startP == -1)
+ startP = 1
+ if (endP == -1)
+ endP = ncol(X)
+ if (is.null(xlab)) {
+ xlab = "index"
+ }
+ if (is.null(ylab)) {
+ ylab = "intensity"
+ }
+ if (is.null(main)) {
+ main = paste(" ", startP + offside, "-", endP + offside)
+ }
+ GraphRange <- c(startP:endP)
+ yn <- X[, GraphRange]
+ if (useLog != -1)
+ yn = log(yn)
+ if (length(yn) > ncol(X))
+ {
+ plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
+ tempVal = trunc(length(GraphRange)/nAxisPos)
+ xPos = c(0:nAxisPos) * tempVal
+ axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
+ for (i in 1:length(levels(groupLabel)))
+ {
+ groupLabelIdx = which(groupLabel == levels(groupLabel)[i])
+ color <- palette(rainbow(length(levels(groupLabel))))
+ for (j in 1:length(groupLabelIdx))
+ {
+ lines(yn[groupLabelIdx[j], ], col = color[i])
+ }
+ }
+ if (!is.null(groupLabel_name))
+ {
+ legendPos = "topleft"
+ legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90")
+ }
+ }
+ if (length(yn) == ncol(X))
+ {
+ plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
+ tempVal = trunc(length(GraphRange)/nAxisPos)
+ xPos = c(0:nAxisPos) * tempVal
+# axis(1, at = xPos, labels = xPos + startP + offside)
+ axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
+ lines(yn)
+ }
+}
\ No newline at end of file
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/Library.Rdata
Binary file nmr_annotation/Library.Rdata has changed
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/ReadMe.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation/ReadMe.txt Tue Jan 30 05:37:10 2018 -0500
@@ -0,0 +1,35 @@
+Instructions to integrate the ""NMR Annotation" tool into a local instance of Galaxy
+Version December 2017 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 "ASICS" library necessary for NMR spectra annotation:
+ - Download package source (*.tar.gz file) from your favorite CRAN (http://www.r-project.org/)
+For example: http://cran.univ-lyon1.fr/
+
+ - Install package in your R session
+install.packages("path/package_name.tar.gz",lib="path",repos=NULL)
+For Example: install.packages("/usr/lib64/R/library/batch_1.1-4.tar",lib="/usr/lib64/R/library",repos=NULL)
+
+ - Finally, load the packages into your R session
+library(batch)
+library(ASICS)
+
+
+## --- Config : --- ##
+ - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add
+
+to create a new section containing the asics_xml tool
+or add
+
+in an existing section
+
+ - Put the two files asics_xml.xml, asics_wrapper.R, all the needeed R functions and the Library.RData (including compound reference spectra) in a same directory
+For example, path=/galaxy/dist/galaxy-dist/tools/annotation
+
+Finally, restart Galaxy
\ No newline at end of file
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/asics_wrapper.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation/asics_wrapper.R Tue Jan 30 05:37:10 2018 -0500
@@ -0,0 +1,191 @@
+#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
+
+## 29122017_asics_wrapper.R
+## Remi Servien, Patrick Tardivel, Marie Tremblay-Franco and Gaelle Lefort
+## marie.tremblay-franco@inra.fr
+
+runExampleL <- FALSE
+
+##------------------------------
+## Options
+##------------------------------
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors=FALSE)
+
+
+##------------------------------
+## Libraries loading
+##------------------------------
+# ParseCommandArgs function
+library(batch)
+library(ASICS)
+
+
+
+# R script call
+source_local <- function(fname)
+{
+argv <- commandArgs(trailingOnly=FALSE)
+base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+source(paste(base_dir, fname, sep="/"))
+}
+#Import the different functions
+source_local("DrawSpec.R")
+
+
+##------------------------------
+## Errors ?????????????????????
+##------------------------------
+
+
+##------------------------------
+## Constants
+##------------------------------
+topEnvC <- environment()
+flagC <- "\n"
+
+
+##------------------------------
+## Script
+##------------------------------
+if(!runExampleL)
+ argLs <- parseCommandArgs(evaluate=FALSE)
+
+# Standards loading
+load(argLs[["standards"]])
+
+## Parameters Loading
+##-------------------
+# Inputs
+## Spectrum to annotate
+zipfile= argLs[["zipfile"]]
+directory=unzip(zipfile, list=F)
+directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
+
+
+##Exclusion zone(s)
+exclusionZones <- argLs[["zone_exclusion_choices.choice"]]
+exclusionZonesBorders <- NULL
+if (!is.null(argLs$zone_exclusion_left))
+{
+ for(i in which(names(argLs)=="zone_exclusion_left"))
+ {
+# exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
+ exclusionZonesBorders <- c(exclusionZonesBorders,argLs[[i]],argLs[[i+1]])
+ }
+}
+
+## Maximal allowed shift
+shift <- argLs[["shift"]]
+
+## Graphical zone(s)
+graphicalZones <- argLs[["zone_graphical_choices.choice"]]
+graphicalZonesBorders <- NULL
+if (!is.null(argLs$zone_exclusion_left))
+{
+ for(i in which(names(argLs)=="zone_graphical_left"))
+ {
+ graphicalZonesBorders <- c(graphicalZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
+ }
+}
+
+# Outputs
+logOut <- argLs[["logOut"]]
+proportionEstimation <- argLs[["proportionEstimation"]]
+graphOut <- argLs[["graphOut"]]
+
+sink(logOut)
+cat("\tPACKAGE INFO\n")
+# pkgs=c("batch", "ASICS")
+pkgs=c("batch", "ASICS")
+for(pkg in pkgs) {
+ suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+ cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
+}
+cat("\n")
+
+
+## Checking arguments
+##-------------------
+error.stock <- "\n"
+if(length(error.stock) > 1)
+ stop(error.stock)
+
+
+## Computation
+##------------
+annotation.Asics <- ASICS(directory, exclusion.areas=matrix(exclusionZonesBorders, byrow=T, ncol=2),
+ max.shift=shift, which.spectra="last", library.metabolites=NULL,
+ threshold.noise=0.02, seed=1234, nb.iter.signif=400)
+
+
+## Saving
+##-------
+# Identified metabolites
+metabolites.estimation <- present_metabolites(annotation.Asics)
+colnames(metabolites.estimation) <- c("Metabolite",colnames(metabolites.estimation)[-1])
+write.table(metabolites.estimation,file=argLs$proportionEstimation,row.names=FALSE,quote=FALSE,sep="\t")
+
+
+## Graphical display
+##------------------
+# Raw and annotated spectra comparison
+pdf(graphOut,onefile=TRUE)
+
+## Graphical output: overlay of raw and estimated spectra
+ppm.metabolites.estimation <- data.frame(round(ppm_grid(annotation.Asics),3),
+ original_mixture(annotation.Asics))
+colnames(ppm.metabolites.estimation) <- c("PPM", "EstimatedProportion")
+ppm.metabolites.estimation <- ppm.metabolites.estimation[order(ppm.metabolites.estimation[,1],decreasing=T), ]
+
+mix <- data.frame(t(ppm.metabolites.estimation[,2]))
+colnames(mix) <- ppm.metabolites.estimation[,1]
+ppm <- ppm.metabolites.estimation[,1]
+
+estimatedMix <- data.frame(round(ppm_grid(annotation.Asics),3), reconstituted_mixture(annotation.Asics))
+colnames(estimatedMix) <- c("PPM","EstimatedProportion")
+estimatedMix <- estimatedMix[order(estimatedMix[,1],decreasing=T), ]
+estimatedMix <- estimatedMix[,2]
+
+## Whole spectra
+GraphRange <- 1:ncol(mix)
+tempVal <- trunc(length(GraphRange)/10)
+xPos <- c(10:0) * tempVal
+plot(1:ncol(mix), mix, type='l', xlab="", main="", xaxt="n", ylab="")
+axis(1, at=xPos, labels=colnames(mix)[xPos + 1])
+lines(estimatedMix, col="red")
+legend("topleft",legend=c("Real Mixture","Estimated Composition"),lty=c(1,1),col=c("black","red"))
+
+## Zoomed spectral window depending on user-selected zone(s)
+graphical.zone.length <- length(graphicalZonesBorders)
+if (graphical.zone.length != 0)
+
+ # par(mfrow=c(2,1))
+for (g in 1:graphical.zone.length)
+ {
+ print(g)
+ plot(1:length((which(round(as.numeric(colnames(mix)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(mix)),2) == max(graphicalZonesBorders[[g]][2],0.5))[1])),
+ mix[(which(round(as.numeric(colnames(mix)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(mix)),2) == max(graphicalZonesBorders[[g]][2],0.5))[1])], type='l', xlab="", ylab="Intensity", main="", xaxt="n")
+ lines(estimatedMix[(which(round(as.numeric(colnames(mix)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(mix)),2) == max(graphicalZonesBorders[[g]][2],0.5))[1])],col="red")
+
+ xPos <- 1
+ nAxisPos <- 4
+ startP <- length(nAxisPos)
+ endP <- length((which(round(as.numeric(colnames(mix)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(mix)),2) == max(graphicalZonesBorders[[g]][2],0.5))[1]))
+ GraphRange <- c(startP:endP)
+ tempVal <- trunc(length(GraphRange)/nAxisPos)
+ xPos <- c(0:nAxisPos) * tempVal
+ noms <- ppm.metabolites.estimation[xPos + which(ppm == round(graphicalZonesBorders[[g]][1],1))[1],1]
+ axis(1, at=xPos, labels=noms)
+ }
+
+invisible(dev.off())
+
+
+## Ending
+##---------------------
+cat("\nEnd of 'NMR annotation' Galaxy module call: ", as.character(Sys.time()), sep="")
+options(stringsAsFactors=strAsFacL)
+rm(list=ls())
+sink()
+
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/asics_xml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation/asics_xml.xml Tue Jan 30 05:37:10 2018 -0500
@@ -0,0 +1,212 @@
+
+
+ Annotation of complex mixture NMR spectra and metabolite proportion estimation
+
+
+ which Rscript ;
+ ## Wrapper
+ Rscript '$__tool_directory__/asics_wrapper.R' standards '$__tool_directory__/Library.Rdata'
+
+ ## Bruker files
+ zipfile $zip_file
+
+ ## Exclusion zone
+ zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
+ #if str($zone_exclusion_choices.choice) == 'yes':
+ #for $i in $zone_exclusion_choices.conditions:
+ zone_exclusion_left ${i.zone_exclusion_left}
+ zone_exclusion_right ${i.zone_exclusion_right}
+ #end for
+ #end if
+
+ ## Maximal shift (spectrum alignement)
+ shift $shift
+
+ ## Graphical zone
+ zone_graphical_choices.choice ${zone_graphical_choices.choice}
+ #if str($zone_graphical_choices.choice) == 'yes':
+ #for $i in $zone_graphical_choices.conditions:
+ zone_graphical_left ${i.zone_graphical_left}
+ zone_graphical_right ${i.zone_graphical_right}
+ #end for
+ #end if
+
+ ## Outputs
+ logOut $logOut
+ proportionEstimation $proportionEstimation
+ graphOut $graphOut
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Patrick Tardivel (patrick.tardivel@inra.fr), Rémi Servien (remi.servien@inra.fr) and Gaelle Lefort (gaelle.lefort@inra.fr)
+
+.. class:: infomark
+
+**Please cite**
+
+Tardivel P., Servien R. and Concordet D. Non asymptotic active set properties of lasso-type estimators in small-dimension (submitted)
+Tardivel P., Servien R., Canlet C., Tremblay-Franco M., Debrauwer L. and Concordet D. ASICS: an automatic method for identification and quantification of metabolites in NMR 1D 1H spectra (in preparation)
+
+---------------------------------------------------
+
+==============
+NMR Annotation
+==============
+
+-----------
+Description
+-----------
+
+ASICS, based on a strong statistical theory, handles automatically the metabolite identification and quantification
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+========================= ================= ======= =========
+Name output file format parameter
+========================= ================= ======= =========
+NA NA NA NA
+========================= ================= ======= =========
+
+
+**Downstream tools**
+
+========================= ================= ======= =========
+Name output file format parameter
+========================= ================= ======= =========
+NA NA NA NA
+========================= ================= ======= =========
+
+
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| Parameter : num + label | Format |
++===========================+============+
+| 1 : Choose your inputs | zip |
++---------------------------+------------+
+
+**Choose your inputs**
+
+You have two methods for your inputs:
+
+ | Zip file : You can put a zip file containing one condition (sample): myinputs.zip.
+
+.. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
+ :width: 800
+
+----------
+Parameters
+----------
+
+Exclusion zone(s)
+| Spectral regions to exclude, water, solvent or contaminant resonances
+| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
+| If NO: no zone to exclude
+| Default value is NO
+|
+
+Left exclusion zone
+| Upper boundary of exclusion zone
+|
+
+Right exclusion zone
+| Lower boundary of exclusion zone
+
+| *Notes:*
+| - these parameters can be used several times using the "Add new exclusion zones" button
+|
+
+Shift
+| Maximum variation of the chemical shift (due to experimental conditions) of a peak of a fixed metabolite allowed in the warping function
+|
+
+Graphical zone(s)
+ | Spectral regions to display
+ | If YES: parameters **Lower graphical zone** and **Upper graphical zone** are visible,
+ | If NO: no zone to display
+ | Default value is NO
+ |
+
+
+------------
+Output files
+------------
+
+proportionEstimation.tsv
+| tabular output
+| Array with p rows (corresponding to the identified metabolites) and 1 column containing the estimated relative intensities
+|
+
+spectra.pdf
+| pdf output
+| Graphical chart of real and estimated spectrum (whole spectral width and zooms depending on exclusion zone(s))
+|
+
+
+---------------------------------------------------
+
+---------------
+Example
+---------------
+
+
+See the W4M00005_mmusculus in the Shared Data/Published Histories menu
+.. image:: ./static/images/NmrAnnotation_ASICS.png
+ :width: 100
+
+
+
+
+
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/static/images/NmrAnnotation_ASICS.png
Binary file nmr_annotation/static/images/NmrAnnotation_ASICS.png has changed
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/test-data/ADG_007.zip
Binary file nmr_annotation/test-data/ADG_007.zip has changed
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/test-data/MTBLS1_177_NMR_Annotation.pdf
Binary file nmr_annotation/test-data/MTBLS1_177_NMR_Annotation.pdf has changed
diff -r 000000000000 -r a8e85c07dc7b nmr_annotation/test-data/MTBLS1_177_NMR_Annotation_proportionEstimation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation/test-data/MTBLS1_177_NMR_Annotation_proportionEstimation.tabular Tue Jan 30 05:37:10 2018 -0500
@@ -0,0 +1,40 @@
+Metabolite Relative_Concentration
+Creatinine 0.0569174516124917
+Citrate 0.0285947900676533
+AceticAcid 0.00931139835139612
+L-Glycine 0.00700618802859799
+ThreonicAcid 0.00312228402191229
+Lactose 0.00274471352269867
+Malonate 0.0026239869463794
+Indoxylsulfate 0.00256983041226207
+L-Arabitol 0.00247809838365845
+L-GlutamicAcid 0.00219750986486448
+Threitol 0.00185008716865122
+L-Alanine 0.00176514469439213
+HippuricAcid 0.00173759535227614
+Betaine 0.00163016358478906
+MalicAcid 0.00154536802871288
+1,3-Diaminopropane 0.00150129592201832
+2-oxoglutarate 0.00142533208121273
+Dimethylamine 0.00131575320617744
+L-Aspartate 0.00127266582522283
+AscorbicAcid 0.00100873973025415
+L-Asparagine 0.00099187237086438
+GuanidinoaceticAcid 0.000925290560878349
+Ethanolamine 0.00089279079362688
+Glycerol 0.00088244833185825
+5,6-Dihydro-5-Methyluracil 0.000849548732878672
+Creatine 0.00079525125560122
+MethylmalonicAcid 0.000792506060661937
+Xylitol 0.000787992683508674
+Taurine 0.000787744798563012
+Succinate 0.000527784171596945
+4-HydroxyphenylAceticAcid 0.000522123163032416
+Methylguanidine 0.000486125204031847
+Myo-Inositol 0.0004425385208034
+beta-HydroxyisovalericAcid 0.000419265217514307
+Propionate 0.000392879831159886
+TMAO 0.000391632855219129
+L-Valine 0.000329117139315598
+Isobutyrate 0.000312582908447652
+CholineChloride 0.000306877971629503