Mercurial > repos > marie-tremblay-metatoul > nmr_annotation
changeset 4:0ff2d9211ebe draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/nmr_annotation commit 3791815505685d0038e392a702860843fe1d443e
| author | marie-tremblay-metatoul |
|---|---|
| date | Fri, 21 Sep 2018 07:42:53 -0400 |
| parents | 9b45c0a33573 |
| children | |
| files | DrawSpec.R Library.Rdata asics_wrapper.R asics_xml.xml nmr_annotation/.gitignore nmr_annotation/.travis.yml nmr_annotation/README.md nmr_annotation/galaxy/nmr_annotation/.shed nmr_annotation/galaxy/nmr_annotation/DrawSpec.R nmr_annotation/galaxy/nmr_annotation/Library.Rdata nmr_annotation/galaxy/nmr_annotation/asics_wrapper.R nmr_annotation/galaxy/nmr_annotation/asics_xml.xml nmr_annotation/galaxy/nmr_annotation/static/images/NmrAnnotation_ASICS.png nmr_annotation/galaxy/nmr_annotation/test-data/ADG_007.zip nmr_annotation/galaxy/nmr_annotation/test-data/MTBLS1_177_NMR_Annotation.pdf nmr_annotation/galaxy/nmr_annotation/test-data/MTBLS1_177_NMR_Annotation_proportionEstimation.tabular static/images/NmrAnnotation_ASICS.png test-data/ADG_007.zip test-data/MTBLS1_177_NMR_Annotation.pdf test-data/MTBLS1_177_NMR_Annotation_proportionEstimation.tabular |
| diffstat | 20 files changed, 538 insertions(+), 614 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DrawSpec.R Fri Sep 21 07:42:53 2018 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/asics_wrapper.R Fri Sep 21 07:42:53 2018 -0400 @@ -0,0 +1,198 @@ +#!/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]]) + } + exclusionZonesBorders <- matrix(exclusionZonesBorders, byrow=T, ncol=2) +} +if (is.null(argLs$zone_exclusion_left)) +{ + exclusionZonesBorders <- matrix(c(0,0), byrow=T, ncol=2) +} +## Maximal allowed shift +shift <- argLs[["shift"]] + +## Graphical zone(s) +graphicalZones <- argLs[["zone_graphical_choices.choice"]] +graphicalZonesBorders <- NULL +if (!is.null(argLs$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) +annotation.Asics <- ASICS(directory, exclusion.areas=exclusionZonesBorders, + 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() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/asics_xml.xml Fri Sep 21 07:42:53 2018 -0400 @@ -0,0 +1,226 @@ +<tool id="NmrAnnotation" name="NMR_Annotation" version="3.0.0"> + + <description> Annotation of complex mixture NMR spectra and metabolite proportion estimation </description> + + <requirements> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.0.1">r-asics</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command><![CDATA[ + ## 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' + ]]></command> + + <inputs> + <param name="zip_file" type="data" format="no_unzip.zip, zip" label="Zip file" /> + + <conditional name="zone_exclusion_choices"> + <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <repeat name="conditions" title="exclusion zones"> + <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" /> + <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" /> + </repeat> + </when> + <when value="no" /> + </conditional> + + <param name="shift" type="float" value="0.01" help="Maximal allowed shift for spectra alignment. Default value is 0.01 ppm" /> + + <conditional name="zone_graphical_choices"> + <param name="choice" type="select" label="Graphical zone(s)" help="Choose if you want to display particular zone(s)" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <repeat name="conditions" title="grapical zones"> + <param name="zone_graphical_left" label="Left graphical zone border" type="float" value="10.0" /> + <param name="zone_graphical_right" label="Right graphical zone border" type="float" value="10.0" /> + </repeat> + </when> + <when value="no" /> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="logOut" label="${tool.name}_log" /> + <data format="tabular" name="proportionEstimation" label="${tool.name}_proportionEstimation" /> + <data format="pdf" name="graphOut" label="${tool.name}_graph" /> + </outputs> + + <tests> + <test> + <param name="zip_file" value="ADG_007.zip" ftype="zip" /> + <output name="proportionEstimation" value="MTBLS1_177_NMR_Annotation_proportionEstimation.tabular" /> + <output name="graphOut" value="MTBLS1_177_NMR_Annotation.pdf" compare="sim_size" delta="300" /> + </test> + </tests> + + <help><![CDATA[ + +.. 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 + +---------- +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 +------- + +.. image:: ./static/images/NmrAnnotation_ASICS.png + + + ]]></help> + + <citations> + <citation type="doi">10.1007/s11306-017-1244-5</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + +</tool>
--- a/nmr_annotation/.gitignore Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -tool_test_output.html -tool_test_output.json -*~
--- a/nmr_annotation/.travis.yml Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - -# This is a special configuration file to run tests on Travis-CI via -# GitHub notifications when changes are committed. -# -# See http://travis-ci.org/ for details -language: python - -before_install: - - sudo apt-get install -y python-virtualenv - - virtualenv planemo-venv - - . planemo-venv/bin/activate - - pip install --upgrade pip setuptools - - pip install planemo - -script: - - planemo lint ${TRAVIS_BUILD_DIR}/galaxy/nmr_annotation/ - - planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch release_17.05 --no_cache_galaxy ${TRAVIS_BUILD_DIR}/galaxy/nmr_annotation/
--- a/nmr_annotation/README.md Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -NMR Annotation for Galaxy -======================== - -[](http://bioconda.github.io) [](https://travis-ci.org/workflow4metabolomics/nmr_annotation) - -Our project ------------ -The [Workflow4Metabolomics](http://workflow4metabolomics.org), W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform. - - -NMR Annotation --------------- -Annotation of complex mixture NMR spectra and metabolite proportion estimation - - -Galaxy ------- -Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. - -Homepage: [https://galaxyproject.org/](https://galaxyproject.org/) - - -Dependencies using Conda ------------------------- -[](http://bioconda.github.io) - -#The main recipe: [https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-speaq](https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-speaq) - -``` -#To install miniconda2 -#http://conda.pydata.org/miniconda.html -#To set an environment: -conda create -n nmr_annotation r-batch r-asics` -#To activate the environment: -. activate nmr_annotation -``` - -[Conda](http://conda.pydata.org/) is package manager that among many other things can be used to manage Python packages. - -Travis ------- -[](https://travis-ci.org/workflow4metabolomics/nmr_annotation) - -Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes! - -Historic contributors ---------------------- - - Marie Tremblay-Franco @mtremblayfr - [French Metabolomics and Fluxomics Infrastructure (MetaboHUB)](http://www.metabohub.fr/en) - [MetaToul](http://www.metatoul.fr/) - - Gildas Le Corguillé @lecorguille - [ABiMS](http://abims.sb-roscoff.fr/) / [IFB](http://www.france-bioinformatique.fr/) - [UPMC](www.upmc.fr)/[CNRS](www.cnrs.fr) - [Station Biologique de Roscoff](http://www.sb-roscoff.fr/) - France
--- a/nmr_annotation/galaxy/nmr_annotation/.shed Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -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
--- a/nmr_annotation/galaxy/nmr_annotation/DrawSpec.R Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -drawSpec <- function (X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1, - xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0) -{ - groupLabel_name = groupLabel - X = as.data.frame(X) -# colnames(X) = c(1:ncol(X)) - X = as.matrix(X) - if (highBound != -1) { - for (i in 1:nrow(X)) { - myIndex = which(X[i, ] > highBound) - X[i, myIndex] = highBound - } - } - if (lowBound != -1) { - for (i in 1:nrow(X)) { - myIndex = which(X[i, ] < lowBound) - X[i, myIndex] = lowBound - } - } - if (is.null(groupLabel)) { - groupLabel = c(1:nrow(X)) - groupLabel = as.factor(groupLabel) - } - else { - levels(groupLabel) = c(1:length(levels(groupLabel))) - } - if (startP == -1) - startP = 1 - if (endP == -1) - endP = ncol(X) - if (is.null(xlab)) { - xlab = "index" - } - if (is.null(ylab)) { - ylab = "intensity" - } - if (is.null(main)) { - main = paste(" ", startP + offside, "-", endP + offside) - } - GraphRange <- c(startP:endP) - yn <- X[, GraphRange] - if (useLog != -1) - yn = log(yn) - if (length(yn) > ncol(X)) - { - plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n") - tempVal = trunc(length(GraphRange)/nAxisPos) - xPos = c(0:nAxisPos) * tempVal - axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside]) - for (i in 1:length(levels(groupLabel))) - { - groupLabelIdx = which(groupLabel == levels(groupLabel)[i]) - color <- palette(rainbow(length(levels(groupLabel)))) - for (j in 1:length(groupLabelIdx)) - { - lines(yn[groupLabelIdx[j], ], col = color[i]) - } - } - if (!is.null(groupLabel_name)) - { - legendPos = "topleft" - legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90") - } - } - if (length(yn) == ncol(X)) - { - plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n") - tempVal = trunc(length(GraphRange)/nAxisPos) - xPos = c(0:nAxisPos) * tempVal -# axis(1, at = xPos, labels = xPos + startP + offside) - axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside]) - lines(yn) - } -} \ No newline at end of file
--- a/nmr_annotation/galaxy/nmr_annotation/asics_wrapper.R Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,198 +0,0 @@ -#!/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$zone_exclusion_left)) -{ - for(i in which(names(argLs)=="zone_exclusion_left")) - { -# exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) - exclusionZonesBorders <- c(exclusionZonesBorders,argLs[[i]],argLs[[i+1]]) - } - exclusionZonesBorders <- matrix(exclusionZonesBorders, byrow=T, ncol=2) -} -if (is.null(argLs$zone_exclusion_left)) -{ - exclusionZonesBorders <- matrix(c(0,0), byrow=T, ncol=2) -} -## Maximal allowed shift -shift <- argLs[["shift"]] - -## Graphical zone(s) -graphicalZones <- argLs[["zone_graphical_choices.choice"]] -graphicalZonesBorders <- NULL -if (!is.null(argLs$zone_exclusion_left)) -{ - for(i in which(names(argLs)=="zone_graphical_left")) - { - graphicalZonesBorders <- c(graphicalZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) - } -} - -# Outputs -logOut <- argLs[["logOut"]] -proportionEstimation <- argLs[["proportionEstimation"]] -graphOut <- argLs[["graphOut"]] - -sink(logOut) -cat("\tPACKAGE INFO\n") -# pkgs=c("batch", "ASICS") -pkgs=c("batch", "ASICS") -for(pkg in pkgs) { - suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) - cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") -} -cat("\n") - - -## Checking arguments -##------------------- -error.stock <- "\n" -if(length(error.stock) > 1) - stop(error.stock) - - -## Computation -##------------ -# annotation.Asics <- ASICS(directory, exclusion.areas=matrix(exclusionZonesBorders, byrow=T, ncol=2), -# max.shift=shift, which.spectra="last", library.metabolites=NULL, -# threshold.noise=0.02, seed=1234, nb.iter.signif=400) -annotation.Asics <- ASICS(directory, exclusion.areas=exclusionZonesBorders, - max.shift=shift, which.spectra="last", library.metabolites=NULL, - threshold.noise=0.02, seed=1234, nb.iter.signif=400) - - -## Saving -##------- -# Identified metabolites -metabolites.estimation <- present_metabolites(annotation.Asics) -colnames(metabolites.estimation) <- c("Metabolite",colnames(metabolites.estimation)[-1]) -write.table(metabolites.estimation,file=argLs$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() -
--- a/nmr_annotation/galaxy/nmr_annotation/asics_xml.xml Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,226 +0,0 @@ -<tool id="NmrAnnotation" name="NMR_Annotation" version="1.0.0"> - - <description> Annotation of complex mixture NMR spectra and metabolite proportion estimation </description> - - <requirements> - <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="1.0.1">r-asics</requirement> - </requirements> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - - <command><![CDATA[ - ## 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' - ]]></command> - - <inputs> - <param name="zip_file" type="data" format="no_unzip.zip, zip" label="Zip file" /> - - <conditional name="zone_exclusion_choices"> - <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <repeat name="conditions" title="exclusion zones"> - <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" /> - <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" /> - </repeat> - </when> - <when value="no" /> - </conditional> - - <param name="shift" type="float" value="0.01" help="Maximal allowed shift for spectra alignment. Default value is 0.01 ppm" /> - - <conditional name="zone_graphical_choices"> - <param name="choice" type="select" label="Graphical zone(s)" help="Choose if you want to display particular zone(s)" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <repeat name="conditions" title="grapical zones"> - <param name="zone_graphical_left" label="Left graphical zone border" type="float" value="10.0" /> - <param name="zone_graphical_right" label="Right graphical zone border" type="float" value="10.0" /> - </repeat> - </when> - <when value="no" /> - </conditional> - </inputs> - - <outputs> - <data format="txt" name="logOut" label="${tool.name}_log" /> - <data format="tabular" name="proportionEstimation" label="${tool.name}_proportionEstimation" /> - <data format="pdf" name="graphOut" label="${tool.name}_graph" /> - </outputs> - - <tests> - <test> - <param name="zip_file" value="ADG_007.zip" ftype="zip" /> - <output name="proportionEstimation" value="MTBLS1_177_NMR_Annotation_proportionEstimation.tabular" /> - <output name="graphOut" value="MTBLS1_177_NMR_Annotation.pdf" compare="sim_size" delta="300" /> - </test> - </tests> - - <help><![CDATA[ - -.. 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 - ----------- -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 -------- - -.. image:: ./static/images/NmrAnnotation_ASICS.png - - - ]]></help> - - <citations> - <citation type="doi">10.1007/s11306-017-1244-5</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> - -</tool>
Binary file nmr_annotation/galaxy/nmr_annotation/test-data/MTBLS1_177_NMR_Annotation.pdf has changed
--- a/nmr_annotation/galaxy/nmr_annotation/test-data/MTBLS1_177_NMR_Annotation_proportionEstimation.tabular Mon Sep 03 08:45:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_177_NMR_Annotation_proportionEstimation.tabular Fri Sep 21 07:42:53 2018 -0400 @@ -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