Mercurial > repos > workflow4metabolomics > camera_combinexsannos
changeset 0:139ff66b0b5d draft
planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464
| author | workflow4metabolomics |
|---|---|
| date | Fri, 26 Jul 2019 16:49:18 -0400 |
| parents | |
| children | ea15115a5b3f |
| files | CAMERA_combinexsAnnos.r README.rst abims_CAMERA_combinexsAnnos.xml lib.r macros.xml repository_dependencies.xml static/images/combinexsannos_variableMetadata.png static/images/combinexsannos_workflow.png static/images/combinexsannos_workflow_zoom.png test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv |
| diffstat | 12 files changed, 1342 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CAMERA_combinexsAnnos.r Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,72 @@ +#!/usr/bin/env Rscript + +# ----- PACKAGE ----- +cat("\tSESSION INFO\n") + +#Import the different functions +source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +source_local("lib.r") + +pkgs=c("CAMERA","multtest","batch") +loadAndDisplayPackages(pkgs) +cat("\n\n"); + +# ----- ARGUMENTS ----- +cat("\tARGUMENTS INFO\n") + +args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(args), col.names=F, quote=F, sep='\t') + +cat("\n\n"); + + +# ----- PROCESSING INFILE ----- +cat("\tINFILE PROCESSING INFO\n") + +#image is an .RData file necessary to use xset variable given by previous tools +load(args$image_pos) +xaP=xa + +diffrepP=NULL +if (exists("diffrep")) diffrepP=diffrep + +load(args$image_neg) +xaN=xa + +diffrepN=NULL +if (exists("diffrep")) diffrepN=diffrep + + +cat("\n\n") + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tARGUMENTS PROCESSING INFO\n") + +# Save arguments to generate a report +if (!exists("listOFargs")) listOFargs=list() +listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] = args + +cat("\n\n") + + +# ----- PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + +cAnnot=combinexsAnnos_function( + xaP=xaP,xaN=xaN, + diffrepP=diffrepP, diffrepN=diffrepN, + pos=args$pos, tol=args$tol,ruleset=args$ruleset, keep_meta=args$keep_meta, + convertRTMinute=args$convertRTMinute, numDigitsMZ=args$numDigitsMZ, numDigitsRT=args$numDigitsRT, + variableMetadataOutput="variableMetadata.tsv" +) + +# ----- EXPORT ----- + +#saving R data in .Rdata file to save the variables used in the present tool +objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile") +save(list=objects2save[objects2save %in% ls()], file="combinexsAnnos.RData") + +cat("\n\n") + +cat("\tDONE\n")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,62 @@ + +Changelog/News +-------------- + +**Version 2.2.5 - 09/04/2019** + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + +- UPGRADE: refactoring of internal code + +**Version 2.2.2 - 01/03/2018** + +- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 + + +**Version 2.0.7 - 29/11/2017** + +- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C + + +**Version 2.0.6 - 10/02/2017** + +- IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate) + + +**Version 2.0.5 - 22/12/2016** + +- IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset) + + +**Version 2.0.4 - 21/04/2016** + +- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 + + +**Version 2.0.3 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- UPDATE: refactoring of internal management of inputs/outputs + + +**Version 2.0.1 - 07/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. + + +**Version 2.0.0 - 09/06/2015** + +- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode + + +Test Status +----------- + +Planemo test using conda: passed + +Planemo test using source env.sh: passed + +Planemo shed_test : passed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_CAMERA_combinexsAnnos.xml Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,267 @@ +<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.5"> + + <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command><![CDATA[ + @COMMAND_RSCRIPT@/CAMERA_combinexsAnnos.r + image_pos '$image_pos' + image_neg '$image_neg' + + pos $pos tol + $tol ruleset + $ruleset keep_meta + $keep_meta + + convertRTMinute $export.convertRTMinute + numDigitsMZ $export.numDigitsMZ + numDigitsRT $export.numDigitsRT + + ]]></command> + + <inputs> + <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" /> + <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" /> + + <param name="pos" type="select" label="Returned peaklist polarity mode"> + <option value="TRUE" selected="true">positive</option> + <option value="FALSE" >negative</option> + </param> + + <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" /> + <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" /> + <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/> + + <section name="export" title="Export options"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + </section> + </inputs> + + <outputs> + <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" /> + <!-- + <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" from_work_dir="combinexsAnnos.RData" /> + --> + </outputs> + + <tests> + <test> + <!-- TODO: generer des vrais dataset pos et neg--> + <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/> + <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/> + <param name="pos" value="TRUE"/> + <param name="tol" value="2"/> + <param name="ruleset" value="1,1"/> + <section name="export"> + <param name="convertRTMinute" value="True"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + </section> + <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> + </test> + </tests> + + + <help><![CDATA[ + +@HELP_AUTHORS@ + +======================= +Xcms.combinexsAnnos +======================= + +----------- +Description +----------- + +**What it does?** + +This function check annotations of ion species with the help of a sample from opposite ion mode. +As first step it searches for pseudospectra from the positive and the negative sample within a reten- +tion time window. For every result the m/z differences between both samples are matched against +specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H +with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are +changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion +mode with recalculated annotations. + +**Details** + +Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno- +tation the resulting peaklist only includes annotation with matches peaks from both mode according +to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is +a two column matrix with includes rule indices from the rule table of both xsAnnotate objects. +A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and +xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined! + + + +----------------- +Workflow position +----------------- + + +**Upstream tools** + +========================= ======================= ===================== ========== +Name Output file Format Parameter +========================= ======================= ===================== ========== +xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file +------------------------- ----------------------- --------------------- ---------- +xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file +========================= ======================= ===================== ========== + +**Downstream tools** + ++---------------------------+-----------------------------------------+--------+ +| Name | Output file | Format | ++===========================+=========================================+========+ +|Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ +|Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ +|Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ +|Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ + + + +The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools: + | Batch_correction + | Filters + | Univariate + | Multivariate PCA, PLS and OPLS + + +**Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow** + +.. image:: combinexsannos_workflow_zoom.png + +**General schema of the metabolomic workflow** + +.. image:: combinexsannos_workflow.png + + +----------- +Input files +----------- + ++---------------------------+----------------------------+ +| Parameter : label | Format | ++===========================+============================+ +| Positive RData ion mode | rdata.camera.positive | ++---------------------------+----------------------------+ +| Negative RData ion mode | rdata.camera.negative | ++---------------------------+----------------------------+ + +------------ +Output files +------------ + +xset.combinexsAnnos.variableMetadata.tsv + + | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results. + | For each metabolite (row) : + | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode + +xset.combinexsAnnos.Rdata + + | Rdata file, that be used outside Galaxy in R. + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +----------- + + | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData** + | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData** + +Parameters +---------- + + | pos -> **positive** + | tol -> **2 (default)** + | ruleset -> **1,1 (default)** + +Output files +------------ + +**Example of an xset.combinexsAnnos.variableMetadata.tsv output:** + +.. image:: combinexsannos_variableMetadata.png + + +--------------------------------------------------- + +Changelog/News +-------------- + +.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS + +**Version 2.2.5 - 09/04/2019** + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + +- UPGRADE: refactoring of internal code + +**Version 2.2.2 - 01/03/2018** + +- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 + +**Version 2.0.7 - 29/11/2017** + +- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C + + +**Version 2.0.6 - 10/02/2017** + +- IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate) + + +**Version 2.0.5 - 22/12/2016** + +- IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset) + +**Version 2.0.4 - 21/04/2016** + +- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 + + +**Version 2.0.3 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- UPDATE: refactoring of internal management of inputs/outputs + + +**Version 2.0.1 - 07/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. + + +**Version 2.0.0 - 09/06/2015** + +- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode + + + ]]></help> + + <expand macro="citation" /> + + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,652 @@ +# lib.r + +#@author G. Le Corguille +# solve an issue with batch if arguments are logical TRUE/FALSE +parseCommandArgs <- function(...) { + args <- batch::parseCommandArgs(...) + for (key in names(args)) { + if (args[key] %in% c("TRUE","FALSE")) + args[key] = as.logical(args[key]) + } + return(args) +} + +#@author G. Le Corguille +# This function will +# - load the packages +# - display the sessionInfo +loadAndDisplayPackages <- function(pkgs) { + for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + + sessioninfo = sessionInfo() + cat(sessioninfo$R.version$version.string,"\n") + cat("Main packages:\n") + for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + cat("Other loaded packages:\n") + for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") +} + +# This function retrieve a xset like object +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + if (is.null(xset@phenoData$sample_group)) + sampclass(xset) = "." + else + sampclass(xset) <- xset@phenoData$sample_group + if (!is.null(xset@phenoData$sample_name)) + rownames(xset@phenoData) = xset@phenoData$sample_name + return (xset) + } +} + +#@author G. Le Corguille +#The function create a pdf from the different png generated by diffreport +diffreport_png2pdf <- function(filebase) { + dir.create("pdf") + + pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf") + pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf") + + system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput)) + system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput)) + +} + +#@author G. Le Corguille +#The function create a zip archive from the different png generated by diffreport +diffreport_png2zip <- function() { + zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip")) + zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip")) +} + +#The function create a zip archive from the different tabular generated by diffreport +diffreport_tabular2zip <- function() { + zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip")) +} + +#@author G. Le Corguille +#This function convert if it is required the Retention Time in minutes +RTSecondToMinute <- function(variableMetadata, convertRTMinute) { + if (convertRTMinute){ + #converting the retention times (seconds) into minutes + print("converting the retention times into minutes in the variableMetadata") + variableMetadata[,"rt"]=variableMetadata[,"rt"]/60 + variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60 + variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60 + } + return (variableMetadata) +} + +#@author G. Le Corguille +#This function format ions identifiers +formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { + splitDeco = strsplit(as.character(variableMetadata$name),"_") + idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) + namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) + variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) + return(variableMetadata) +} + +#The function annotateDiffreport without the corr function which bugs +annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") { + # Resolve the bug with x11, with the function png + options(bitmapType='cairo') + + #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped. + res=try(is.null(xset@filled)) + + # ------ annot ------- + args$calcCiS=as.logical(args$calcCiS) + args$calcIso=as.logical(args$calcIso) + args$calcCaS=as.logical(args$calcCaS) + + # common parameters + args4annotate = list(object=xset, + nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm, + maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac, + ppm=args$ppm,mzabs=args$mzabs,quick=args$quick, + polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval) + + # quick == FALSE + if(args$quick==FALSE) { + args4annotate = append(args4annotate, + list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval, + calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS)) + # no ruleset + if (!is.null(args$multiplier)) { + args4annotate = append(args4annotate, + list(multiplier=args$multiplier)) + } + # ruleset + else { + rulset=read.table(args$rules, h=T, sep=";") + if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t") + if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",") + if (ncol(rulset) < 4) { + error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation" + print(error_message) + stop(error_message) + } + + args4annotate = append(args4annotate, + list(rules=rulset)) + } + } + + + # launch annotate + xa = do.call("annotate", args4annotate) + peakList=getPeaklist(xa,intval=args$intval) + peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); + + # --- Multi condition : diffreport --- + diffrepOri=NULL + if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) { + #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped. + res=try(is.null(xset@filled)) + classes=levels(sampclass(xset)) + x=1:(length(classes)-1) + for (i in seq(along=x) ) { + y=1:(length(classes)) + for (n in seq(along=y)){ + if(i+n <= length(classes)){ + filebase=paste(classes[i],class2=classes[i+n],sep="-vs-") + + diffrep=diffreport( + object=xset,class1=classes[i],class2=classes[i+n], + filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth, + sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0) + + diffrepOri = diffrep + + # renamming of the column rtmed to rt to fit with camera peaklist function output + colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt" + colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz" + + # combines results and reorder columns + diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F) + diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))]) + + diffrep = RTSecondToMinute(diffrep, args$convertRTMinute) + diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ) + + if(args$sortpval){ + diffrep=diffrep[order(diffrep$pvalue), ] + } + + dir.create("tabular", showWarnings = FALSE) + write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep="")) + + if (args$eicmax != 0) { + if (args$png2 == "pdf") + diffreport_png2pdf(filebase) + } + } + } + } + if (args$png2 == "zip") + diffreport_png2zip() + if (args$tabular2 == "zip") + diffreport_tabular2zip() + } + + # --- variableMetadata --- + variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] + variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute) + variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ) + # if we have 2 conditions, we keep stat of diffrep + if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) { + variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F) + if(exists("args[[\"sortpval\"]]")){ + variableMetadata=variableMetadata[order(variableMetadata$pvalue), ] + } + } + + variableMetadataOri=variableMetadata + write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) + + return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri)); + +} + + +combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL, + pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, + numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){ + + #Load the two Rdata to extract the xset objects from positive and negative mode + cat("\tObject xset from positive mode\n") + print(xaP) + cat("\n") + + cat("\tObject xset from negative mode\n") + print(xaN) + cat("\n") + + cat("\n") + cat("\tCombining...\n") + #Convert the string to numeric for creating matrix + row=as.numeric(strsplit(ruleset,",")[[1]][1]) + column=as.numeric(strsplit(ruleset,",")[[1]][2]) + ruleset=cbind(row,column) + #Test if the file comes from an older version tool + if ((!is.null(xaP)) & (!is.null(xaN))) { + #Launch the combinexsannos function from CAMERA + cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset) + } else { + stop("You must relauch the CAMERA.annotate step with the lastest version.") + } + + if(pos){ + xa=xaP + mode="neg. Mode" + } else { + xa=xaN + mode="pos. Mode" + } + + peakList=getPeaklist(xa) + peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); + variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]); + variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))] + + #Test if there are more than two classes (conditions) + if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) { + diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="") + diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="") + + variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name") + variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name") + } + + rownames(variableMetadata) = NULL + #TODO: checker + #colnames(variableMetadata)[1:2] = c("name","mz/rt"); + + variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute) + variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) + + #If the user want to keep only the metabolites which match a difference + if(keep_meta){ + variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",] + } + + #Write the output into a tsv file + write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) + return(variableMetadata); + +} + +# This function get the raw file path from the arguments +getRawfilePathFromArguments <- function(singlefile, zipfile, args) { + if (!is.null(args$zipfile)) zipfile = args$zipfile + if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive + if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative + + if (!is.null(args$singlefile_galaxyPath)) { + singlefile_galaxyPaths = args$singlefile_galaxyPath; + singlefile_sampleNames = args$singlefile_sampleName + } + if (!is.null(args$singlefile_galaxyPathPositive)) { + singlefile_galaxyPaths = args$singlefile_galaxyPathPositive; + singlefile_sampleNames = args$singlefile_sampleNamePositive + } + if (!is.null(args$singlefile_galaxyPathNegative)) { + singlefile_galaxyPaths = args$singlefile_galaxyPathNegative; + singlefile_sampleNames = args$singlefile_sampleNameNegative + } + if (exists("singlefile_galaxyPaths")){ + singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,",")) + singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,",")) + + singlefile=NULL + for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { + singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i] + singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i] + singlefile[[singlefile_sampleName]] = singlefile_galaxyPath + } + } + for (argument in c("zipfile", "zipfilePositive", "zipfileNegative", + "singlefile_galaxyPath", "singlefile_sampleName", + "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive", + "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { + args[[argument]]=NULL + } + return(list(zipfile=zipfile, singlefile=singlefile, args=args)) +} + + +# This function retrieve the raw file in the working directory +# - if zipfile: unzip the file with its directory tree +# - if singlefiles: set symlink with the good filename +retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { + if(!is.null(singlefile) && (length("singlefile")>0)) { + for (singlefile_sampleName in names(singlefile)) { + singlefile_galaxyPath = singlefile[[singlefile_sampleName]] + if(!file.exists(singlefile_galaxyPath)){ + error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") + print(error_message); stop(error_message) + } + + file.symlink(singlefile_galaxyPath,singlefile_sampleName) + } + directory = "." + + } + if(!is.null(zipfile) && (zipfile!="")) { + if(!file.exists(zipfile)){ + error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") + print(error_message) + stop(error_message) + } + + #list all file in the zip file + #zip_files=unzip(zipfile,list=T)[,"Name"] + + #unzip + suppressWarnings(unzip(zipfile, unzip="unzip")) + + #get the directory name + filesInZip=unzip(zipfile, list=T); + directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); + directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] + directory = "." + if (length(directories) == 1) directory = directories + + cat("files_root_directory\t",directory,"\n") + + } + return (directory) +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524 +# https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd +############################################################ +## getEIC +getEIC <- function(object, mzrange, rtrange = 200, + groupidx, sampleidx = sampnames(object), + rt = c("corrected", "raw")) { + + files <- filepaths(object) + grp <- groups(object) + samp <- sampnames(object) + prof <- profinfo(object) + + rt <- match.arg(rt) + + if (is.numeric(sampleidx)) + sampleidx <- sampnames(object)[sampleidx] + sampidx <- match(sampleidx, sampnames(object)) + + if (!missing(groupidx)) { + if (is.numeric(groupidx)) + groupidx <- groupnames(object)[unique(as.integer(groupidx))] + grpidx <- match(groupidx, groupnames(object, template = groupidx)) + } + + if (missing(mzrange)) { + if (missing(groupidx)) + stop("No m/z range or groups specified") + if (any(is.na(groupval(object, value = "mz")))) + warning( + "`NA` values in xcmsSet. Use fillPeaks() on the object to fill", + "-in missing peak values. Note however that this will also ", + "insert intensities of 0 for peaks that can not be filled in.") + mzmin <- apply(groupval(object, value = "mzmin"), 1, min, na.rm = TRUE) + mzmax <- apply(groupval(object, value = "mzmax"), 1, max, na.rm = TRUE) + mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2) + ## if (any(is.na(groupval(object, value = "mz")))) + ## stop('Please use fillPeaks() to fill up NA values !') + ## mzmin <- -rowMax(-groupval(object, value = "mzmin")) + ## mzmax <- rowMax(groupval(object, value = "mzmax")) + ## mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2) + } else if (all(c("mzmin","mzmax") %in% colnames(mzrange))) + mzrange <- mzrange[,c("mzmin", "mzmax"),drop=FALSE] + else if (is.null(dim(mzrange))) + stop("mzrange must be a matrix") + colnames(mzrange) <- c("mzmin", "mzmax") + + if (length(rtrange) == 1) { + if (missing(groupidx)) + rtrange <- matrix(rep(range(object@rt[[rt]][sampidx]), nrow(mzrange)), + ncol = 2, byrow = TRUE) + else { + rtrange <- retexp(grp[grpidx,c("rtmin","rtmax"),drop=FALSE], rtrange) + } + } else if (is.null(dim(rtrange))) + stop("rtrange must be a matrix or single number") + colnames(rtrange) <- c("rtmin", "rtmax") + + ## Ensure that we've got corrected retention time if requested. + if (is.null(object@rt[[rt]])) + stop(rt, " retention times not present in 'object'!") + + ## Ensure that the defined retention time range is within the rtrange of the + ## object: we're using the max minimal rt of all files and the min maximal rt + rtrs <- lapply(object@rt[[rt]], range) + rtr <- c(max(unlist(lapply(rtrs, "[", 1))), + min(unlist(lapply(rtrs, "[", 2)))) + ## Check if we've got a range which is completely off: + if (any(rtrange[, "rtmin"] >= rtr[2] | rtrange[, "rtmax"] <= rtr[1])) { + outs <- which(rtrange[, "rtmin"] >= rtr[2] | + rtrange[, "rtmax"] <= rtr[1]) + stop(length(outs), " of the specified 'rtrange' are completely outside ", + "of the retention time range of 'object' which is (", rtr[1], ", ", + rtr[2], "). The first was: (", rtrange[outs[1], "rtmin"], ", ", + rtrange[outs[1], "rtmax"], "!") + } + lower_rt_outside <- rtrange[, "rtmin"] < rtr[1] + upper_rt_outside <- rtrange[, "rtmax"] > rtr[2] + if (any(lower_rt_outside) | any(upper_rt_outside)) { + ## Silently fix these ranges. + rtrange[lower_rt_outside, "rtmin"] <- rtr[1] + rtrange[upper_rt_outside, "rtmax"] <- rtr[2] + } + + if (missing(groupidx)) + gnames <- character(0) + else + gnames <- groupidx + + eic <- vector("list", length(sampleidx)) + names(eic) <- sampleidx + + for (i in seq(along = sampidx)) { + + ## cat(sampleidx[i], "") + flush.console() + ## getXcmsRaw takes care of rt correction, susetting to scanrage and other + ## stuff. + lcraw <- getXcmsRaw(object, sampleidx = sampidx[i], rt=rt) + currenteic <- xcms::getEIC(lcraw, mzrange, rtrange, step = prof$step) + eic[[i]] <- currenteic@eic[[1]] + rm(lcraw) + gc() + } + ## cat("\n") + + invisible(new("xcmsEIC", eic = eic, mzrange = mzrange, rtrange = rtrange, + rt = rt, groupnames = gnames)) +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524 +# https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd +############################################################ +## diffreport +diffreport = function(object, + class1 = levels(sampclass(object))[1], + class2 = levels(sampclass(object))[2], + filebase = character(), + eicmax = 0, eicwidth = 200, + sortpval = TRUE, + classeic = c(class1,class2), + value = c("into","maxo","intb"), + metlin = FALSE, + h = 480, w = 640, mzdec=2, + missing = numeric(), ...) { + + if ( nrow(object@groups)<1 || length(object@groupidx) <1) { + stop("No group information. Use group().") + } + + if (!is.numeric(w) || !is.numeric(h)) + stop("'h' and 'w' have to be numeric") + ## require(multtest) || stop("Couldn't load multtest") + + value <- match.arg(value) + groupmat <- groups(object) + if (length(groupmat) == 0) + stop("No group information found") + samples <- sampnames(object) + n <- length(samples) + classlabel <- sampclass(object) + classlabel <- levels(classlabel)[as.vector(unclass(classlabel))] + + values <- groupval(object, "medret", value=value) + indecies <- groupval(object, "medret", value = "index") + + if (!all(c(class1,class2) %in% classlabel)) + stop("Incorrect Class Labels") + + ## c1 and c2 are column indices of class1 and class2 resp. + c1 <- which(classlabel %in% class1) + c2 <- which(classlabel %in% class2) + ceic <- which(classlabel %in% classeic) + if (length(intersect(c1, c2)) > 0) + stop("Intersecting Classes") + + ## Optionally replace NA values with the value provided with missing + if (length(missing)) { + if (is.numeric(missing)) { + ## handles NA, Inf and -Inf + values[, c(c1, c2)][!is.finite(values[, c(c1, c2)])] <- missing[1] + } else + stop("'missing' should be numeric") + } + ## Check against missing Values + if (any(is.na(values[, c(c1, c2)]))) + warning("`NA` values in xcmsSet. Use fillPeaks() on the object to fill", + "-in missing peak values. Note however that this will also ", + "insert intensities of 0 for peaks that can not be filled in.") + + mean1 <- rowMeans(values[,c1,drop=FALSE], na.rm = TRUE) + mean2 <- rowMeans(values[,c2,drop=FALSE], na.rm = TRUE) + + ## Calculate fold change. + ## For foldchange <1 set fold to 1/fold + ## See tstat to check which was higher + fold <- mean2 / mean1 + fold[!is.na(fold) & fold < 1] <- 1/fold[!is.na(fold) & fold < 1] + + testval <- values[,c(c1,c2)] + ## Replace eventual infinite values with NA (CAMERA issue #33) + testval[is.infinite(testval)] <- NA + testclab <- c(rep(0,length(c1)),rep(1,length(c2))) + + if (min(length(c1), length(c2)) >= 2) { + tstat <- mt.teststat(testval, testclab, ...) + pvalue <- xcms:::pval(testval, testclab, tstat) + } else { + message("Too few samples per class, skipping t-test.") + tstat <- pvalue <- rep(NA,nrow(testval)) + } + stat <- data.frame(fold = fold, tstat = tstat, pvalue = pvalue) + if (length(levels(sampclass(object))) >2) { + pvalAnova<-c() + for(i in 1:nrow(values)){ + var<-as.numeric(values[i,]) + ano<-summary(aov(var ~ sampclass(object)) ) + pvalAnova<-append(pvalAnova, unlist(ano)["Pr(>F)1"]) + } + stat<-cbind(stat, anova= pvalAnova) + } + if (metlin) { + neutralmass <- groupmat[,"mzmed"] + ifelse(metlin < 0, 1, -1) + metlin <- abs(metlin) + digits <- ceiling(-log10(metlin))+1 + metlinurl <- + paste("http://metlin.scripps.edu/simple_search_result.php?mass_min=", + round(neutralmass - metlin, digits), "&mass_max=", + round(neutralmass + metlin, digits), sep="") + values <- cbind(metlin = metlinurl, values) + } + twosamp <- cbind(name = groupnames(object), stat, groupmat, values) + if (sortpval) { + tsidx <- order(twosamp[,"pvalue"]) + twosamp <- twosamp[tsidx,] + rownames(twosamp) <- 1:nrow(twosamp) + values<-values[tsidx,] + } else + tsidx <- 1:nrow(values) + + if (length(filebase)) + write.table(twosamp, paste(filebase, ".tsv", sep = ""), quote = FALSE, sep = "\t", col.names = NA) + + if (eicmax > 0) { + if (length(unique(peaks(object)[,"rt"])) > 1) { + ## This looks like "normal" LC data + + eicmax <- min(eicmax, length(tsidx)) + eics <- getEIC(object, rtrange = eicwidth*1.1, sampleidx = ceic, + groupidx = tsidx[seq(length = eicmax)]) + + if (length(filebase)) { + eicdir <- paste(filebase, "_eic", sep="") + boxdir <- paste(filebase, "_box", sep="") + dir.create(eicdir) + dir.create(boxdir) + if (capabilities("png")){ + xcms:::xcmsBoxPlot(values[seq(length = eicmax),], + sampclass(object), dirpath=boxdir, pic="png", width=w, height=h) + png(file.path(eicdir, "%003d.png"), width = w, height = h) + } else { + xcms:::xcmsBoxPlot(values[seq(length = eicmax),], + sampclass(object), dirpath=boxdir, pic="pdf", width=w, height=h) + pdf(file.path(eicdir, "%003d.pdf"), width = w/72, + height = h/72, onefile = FALSE) + } + } + plot(eics, object, rtrange = eicwidth, mzdec=mzdec) + + if (length(filebase)) + dev.off() + } else { + ## This looks like a direct-infusion single spectrum + if (length(filebase)) { + eicdir <- paste(filebase, "_eic", sep="") + boxdir <- paste(filebase, "_box", sep="") + dir.create(eicdir) + dir.create(boxdir) + if (capabilities("png")){ + xcmsBoxPlot(values[seq(length = eicmax),], + sampclass(object), dirpath=boxdir, pic="png", + width=w, height=h) + png(file.path(eicdir, "%003d.png"), width = w, height = h, + units = "px") + } else { + xcmsBoxPlot(values[seq(length = eicmax),], + sampclass(object), dirpath=boxdir, pic="pdf", + width=w, height=h) + pdf(file.path(eicdir, "%003d.pdf"), width = w/72, + height = h/72, onefile = FALSE) + } + } + + plotSpecWindow(object, gidxs = tsidx[seq(length = eicmax)], borderwidth=1) + + if (length(filebase)) + dev.off() + } + } + + invisible(twosamp) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,168 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.4_3">r-snow</requirement> + <requirement type="package" version="1.38.1">bioconductor-camera</requirement> + <requirement type="package" version="2.38.0">bioconductor-multtest</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.3.31">graphicsmagick</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + </xml> + + <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token> + + <!-- raw file load for planemo test --> + <token name="@COMMAND_FILE_LOAD@"> + #if $file_load_section.file_load_conditional.file_load_select == "yes": + #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #else + zipfile '$file_load_section.file_load_conditional.input' + #end if + #end if + </token> + + <xml name="input_file_load"> + <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> + <conditional name="file_load_conditional"> + <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" >yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> + </when> + </conditional> + </section> + </xml> + + <xml name="test_file_load_zip"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> + </conditional> + </section> + </xml> + + <xml name="test_file_load_single"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + </conditional> + </section> + </xml> + + <!-- peaklist export option management --> + <token name="@COMMAND_PEAKLIST@"> + convertRTMinute $export.convertRTMinute + numDigitsMZ $export.numDigitsMZ + numDigitsRT $export.numDigitsRT + intval $export.intval + </token> + + <xml name="input_peaklist"> + <section name="export" title="Export options"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below"> + <option value="into" selected="true">into</option> + <option value="maxo" >maxo</option> + <option value="intb">intb</option> + </param> + </section> + </xml> + + <xml name="test_peaklist"> + <section name="export"> + <param name="convertRTMinute" value="True"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + <param name="intval" value="into"/> + </section> + </xml> + + <!-- annotate_diffreport <test> commun part --> + <xml name="test_annotate_diffreport"> + <section name="groupfwhm"> + <param name="sigma" value="6"/> + <param name="perfwhm" value="0.6"/> + </section> + <section name="findisotopes"> + <param name="maxcharge" value="3"/> + <param name="maxiso" value="4"/> + <param name="minfrac" value="0.5"/> + </section> + <section name="findgeneral"> + <param name="ppm" value="5"/> + <param name="mzabs" value="0.015"/> + <param name="max_peaks" value="100"/> + </section> + <section name="diffreport"> + <conditional name="options"> + <param name="option" value="show"/> + <param name="eicmax" value="200"/> + <param name="eicwidth" value="200"/> + <param name="value" value="into"/> + <param name="h" value="480"/> + <param name="w" value="640"/> + <param name="mzdec" value="2"/> + <param name="sortpval" value="False"/> + </conditional> + </section> + <expand macro="test_peaklist"/> + </xml> + + <xml name="test_annotate_quick_false"> + <param name="quick" value="FALSE"/> + <section name="groupcorr"> + <param name="cor_eic_th" value="0.75"/> + <param name="graphMethod" value="hcs"/> + <param name="pval" value="0.05"/> + <param name="calcCiS" value="True"/> + <param name="calcIso" value="False"/> + <param name="calcCaS" value="False"/> + </section> + </xml> + + <xml name="test_annotate_quick_true"> + <conditional name="quick_block"> + <param name="quick" value="TRUE"/> + </conditional> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +--------------------------------------------------- + + </token> + + + <xml name="citation"> + <citations> + <citation type="doi">10.1021/ac202450g</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,5 @@ +<?xml version="1.0" ?> +<repositories> + <repository changeset_revision="4a51ab3d8ecf" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> +</repositories> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,116 @@ +name namecustom mz mzmin mzmax rt rtmin rtmax npeaks KO WT isotopes adduct pcgroup isotopes.1 adduct.1 pcgroup.1 neg. Mode +M208T3291 M207.8T54.9 207.800003051758 207.800003051758 207.800003051758 54.8548661171705 54.8548661171705 54.8548661171705 1 1 0 2102 [M+H]+ 206.793 2102 Found [M+H]+/[M-H]- +M210T3110 M210.2T51.8 210.199996948242 210.199996948242 210.199996948242 51.8351814475023 51.8351814475023 51.8351814475023 1 1 0 5340 [M+H]+ 209.193 5340 Found [M+H]+/[M-H]- +M228T3846 M228.2T64.1 228.199996948242 228.199996948242 228.199996948242 64.1004477702677 64.0786131787182 64.1222823618172 2 1 1 [M+H-C6H8O6]+ 403.216 [M+2H-NH3]2+ 471.41 21 [M+H]+ 227.193 21 Found [M+H]+/[M-H]- +M235T3976 M234.9T66.3 234.900009155273 234.900009155273 234.900009155273 66.2671959497008 66.2671959497008 66.2671959497008 1 0 1 2000 [M+H]+ 233.893 2000 Found [M+H]+/[M-H]- +M236T3873 M236.2T64.5 236.199996948242 236.199996948242 236.199996948242 64.5417430278147 64.5417430278147 64.5417430278147 1 0 1 2733 [M+H]+ 235.193 2733 Found [M+H]+/[M-H]- +M238T2755 M238.2T45.9 238.199996948242 238.199996948242 238.199996948242 45.9108043388673 45.9108043388673 45.9108043388673 1 0 1 4595 [M+H]+ 237.193 4595 Found [M+H]+/[M-H]- +M239T4130 M239T68.8 239 239 239 68.8389740321595 68.8389740321595 68.8389740321595 1 0 1 1473 [M+H]+ 237.993 1473 Found [M+H]+/[M-H]- +M250T4052 M250.2T67.5 250.199996948242 250.199996948242 250.199996948242 67.5268251014762 67.5268251014762 67.5268251014762 1 1 0 77 [M+H]+ 249.193 77 Found [M+H]+/[M-H]- +M258T3448 M258.2T57.5 258.200012207031 258.200012207031 258.200012207031 57.4710855711383 57.4427244480407 57.4994466942358 2 1 1 2922 [M+H]+ 257.193 2922 Found [M+H]+/[M-H]- +M261T2686 M261.2T44.8 261.200012207031 261.200012207031 261.200012207031 44.7613459684195 44.7613459684195 44.7613459684195 1 0 1 640 [M+H]+ 260.193 640 Found [M+H]+/[M-H]- +M266T3323 M266.4T55.4 266.399993896484 266.399993896484 266.399993896484 55.3795249542604 55.3795249542604 55.3795249542604 1 0 1 16 [M+H]+ 265.393 16 Found [M+H]+/[M-H]- +M275T2920 M275.2T48.7 275.200012207031 275.200012207031 275.200012207031 48.671416116166 48.671416116166 48.671416116166 1 0 1 2868 [M+H]+ 274.193 2868 Found [M+H]+/[M-H]- +M276T3867_1 M275.9T64.4_1 275.899993896484 275.899993896484 275.899993896484 64.4483155999427 64.4483155999427 64.4483155999427 1 1 0 21 [M+H]+ 274.893 21 Found [M+H]+/[M-H]- +M276T2603 M276.2T43.4 276.200012207031 276.200012207031 276.200012207031 43.3808995766058 43.3808995766058 43.3808995766058 1 1 0 5243 [M+H]+ 275.193 5243 Found [M+H]+/[M-H]- +M284T3653 M284.1T60.9 284.100006103516 284.100006103516 284.100006103516 60.8809514467087 60.8809514467087 60.8809514467087 1 1 0 [M+H-CH3]+ 298.114 47 [M+H]+ 283.093 47 Found [M+H]+/[M-H]- +M287T4128 M287.1T68.8 287.100006103516 287.100006103516 287.100006103516 68.8074238019644 68.8074238019644 68.8074238019644 1 1 0 23 [M+H]+ 286.093 23 Found [M+H]+/[M-H]- +M304T3912 M304T65.2 304 304 304 65.195563930308 65.195563930308 65.195563930308 1 0 1 4817 [M+H]+ 302.993 4817 Found [M+H]+/[M-H]- +M304T2622 M304T43.7 304 304 304 43.697161463341 43.697161463341 43.697161463341 1 0 1 2642 [M+H]+ 302.993 2642 Found [M+H]+/[M-H]- +M310T3484 M310.2T58.1 310.200012207031 310.200012207031 310.200012207031 58.0652451156923 58.0652451156923 58.0652451156923 1 1 0 [M+H-H20]+ 327.208 31 [M+H]+ 309.193 31 Found [M+H]+/[M-H]- +M311T3667 M311.2T61.1 311.200012207031 311.200012207031 311.200012207031 61.1232252152794 61.1232252152794 61.1232252152794 1 1 0 [M+H]+ 310.189 2 [M+H]+ 310.189 2 Found [M+H]+/[M-H]- +M317T4122 M317T68.7 317 317 317 68.7029543960126 68.7029543960126 68.7029543960126 1 1 0 1716 [M+H]+ 315.993 1716 Found [M+H]+/[M-H]- +M319T3963 M319.3T66.1 319.300018310547 319.300018310547 319.300018310547 66.0540795330602 66.0540795330602 66.0540795330602 1 0 1 1982 [M+H]+ 318.293 1982 Found [M+H]+/[M-H]- +M326T3910 M326.3T65.2 326.300018310547 326.300018310547 326.300018310547 65.1694320732506 65.1694320732506 65.1694320732506 1 0 1 4822 [M+H]+ 325.293 4822 Found [M+H]+/[M-H]- +M329T3539 M329T59 329 329 329 58.976324193497 58.976324193497 58.976324193497 1 0 1 1952 [M+H]+ 327.993 1952 Found [M+H]+/[M-H]- +M330T3500 M330.2T58.3 330.200012207031 330.200012207031 330.200012207031 58.3366734462018 58.279218107523 58.3941287848805 2 1 1 [2M+Na+K]2+ 299.215 76 [M+H]+ 329.193 76 Found [M+H]+/[M-H]- +M333T3521 M333T58.7 333 333 333 58.6762856708046 58.6762856708046 58.6762856708046 1 0 1 368 [M+H]+ 331.993 368 Found [M+H]+/[M-H]- +M341T3309 M341.2T55.1 341.200012207031 341.200012207031 341.200012207031 55.1430121663691 55.1430121663691 55.1430121663691 1 0 1 4 [M+H]+ 340.193 4 Found [M+H]+/[M-H]- +M341T4172 M341.4T69.5 341.399993896484 341.399993896484 341.399993896484 69.5403852759756 69.5403852759756 69.5403852759756 1 1 0 4369 [M+H]+ 340.393 4369 Found [M+H]+/[M-H]- +M342T3038 M342.3T50.6 342.300018310547 342.300018310547 342.300018310547 50.6358552925949 50.6358552925949 50.6358552925949 1 0 1 3220 [M+H]+ 341.293 3220 Found [M+H]+/[M-H]- +M345T3788 M345T63.1 345 345 345 63.1344882463539 63.1344882463539 63.1344882463539 1 0 1 4445 [M+H]+ 343.993 4445 Found [M+H]+/[M-H]- +M348T3493 M348.2T58.2 348.200012207031 348.200012207031 348.200012207031 58.2199122659174 58.1464333812605 58.2666138953485 3 1 2 31 [M+H]+ 347.193 31 Found [M+H]+/[M-H]- +M349T4038 M348.9T67.3 348.899993896484 348.899993896484 348.899993896484 67.3077590567051 67.3077590567051 67.3077590567051 1 0 1 3765 [M+H]+ 347.893 3765 Found [M+H]+/[M-H]- +M350T3215 M350T53.6 350 350 350 53.5773282247933 53.5773282247933 53.5773282247933 1 1 0 4315 [M+H]+ 348.993 4315 Found [M+H]+/[M-H]- +M350T3484 M350.2T58.1 350.200012207031 350.200012207031 350.200012207031 58.0691763348732 58.0691763348732 58.0691763348732 1 0 1 [41][M]+ [M+Na]+ 327.208 31 [41][M]+ [M+H]+ 349.193 31 Found [M+H]+/[M-H]- +M354T4176 M354.3T69.6 354.300018310547 354.300018310547 354.300018310547 69.6081394901155 69.6081394901155 69.6081394901155 1 0 1 4388 [M+H]+ 353.293 4388 Found [M+H]+/[M-H]- +M361T3500 M361T58.3 361 361 361 58.3317289697945 58.3317289697945 58.3317289697945 1 1 0 3374 [M+H]+ 359.993 3374 Found [M+H]+/[M-H]- +M362T3394 M362.3T56.6 362.300018310547 362.300018310547 362.300018310547 56.5744464204614 56.5744464204614 56.5744464204614 1 0 1 502 [M+H]+ 361.293 502 Found [M+H]+/[M-H]- +M363T3890 M363T64.8 363 363 363 64.8295865475032 64.8295865475032 64.8295865475032 1 0 1 2235 [M+H]+ 361.993 2235 Found [M+H]+/[M-H]- +M369T4287 M369.1T71.4 369.100006103516 369.100006103516 369.100006103516 71.4477203793839 71.4477203793839 71.4477203793839 1 1 0 6094 [M+H]+ 368.093 6094 Found [M+H]+/[M-H]- +M371T4218 M371.3T70.3 371.300018310547 371.300018310547 371.300018310547 70.2994362565411 70.2994362565411 70.2994362565411 1 1 0 5327 [M+H]+ 370.293 5327 Found [M+H]+/[M-H]- +M372T4221 M372.3T70.4 372.300018310547 372.300018310547 372.300018310547 70.3555724833019 70.3555724833019 70.3555724833019 1 0 1 5985 [M+H]+ 371.293 5985 Found [M+H]+/[M-H]- +M375T2994 M375.2T49.9 375.200012207031 375.200012207031 375.200012207031 49.9011643160422 49.9011643160422 49.9011643160422 1 0 1 32 [M+H]+ 374.193 32 Found [M+H]+/[M-H]- +M378T3345 M377.9T55.7 377.899993896484 377.899993896484 377.899993896484 55.7479583772851 55.7479583772851 55.7479583772851 1 1 0 802 [M+H]+ 376.893 802 Found [M+H]+/[M-H]- +M396T4099 M396.3T68.3 396.300018310547 396.300018310547 396.300018310547 68.3110839411979 68.3110839411979 68.3110839411979 2 1 0 150 [M+H]+ 395.293 150 Found [M+H]+/[M-H]- +M399T3288 M399T54.8 399 399 399 54.7925197533959 54.7925197533959 54.7925197533959 1 0 1 2111 [M+H]+ 397.993 2111 Found [M+H]+/[M-H]- +M404T2691 M404.1T44.8 404.100006103516 404.100006103516 404.100006103516 44.8428547027469 44.8428547027469 44.8428547027469 1 0 1 [M+H-H20]+ 421.11 6 [M+H]+ 403.093 6 Found [M+H]+/[M-H]- +M406T3575 M406T59.6 406 406 406 59.5771690581316 59.5771690581316 59.5771690581316 1 0 1 1668 [M+H]+ 404.993 1668 Found [M+H]+/[M-H]- +M408T3956 M408.3T65.9 408.300018310547 408.300018310547 408.300018310547 65.9308188818822 65.9308188818822 65.9308188818822 1 1 0 5459 [M+H]+ 407.293 5459 Found [M+H]+/[M-H]- +M413T4059 M413T67.7 413 413 413 67.65694615063 67.65694615063 67.65694615063 1 0 1 4700 [M+H]+ 411.993 4700 Found [M+H]+/[M-H]- +M415T3626 M415.2T60.4 415.200012207031 415.200012207031 415.200012207031 60.4314954588001 60.4314954588001 60.4314954588001 1 1 0 26 [M+H]+ 414.193 26 Found [M+H]+/[M-H]- +M418T3317 M418.4T55.3 418.399993896484 418.399993896484 418.399993896484 55.281978863019 55.281978863019 55.281978863019 1 0 1 539 [M+H]+ 417.393 539 Found [M+H]+/[M-H]- +M420T4187 M420.4T69.8 420.399993896484 420.399993896484 420.399993896484 69.7759636871153 69.7759636871153 69.7759636871153 1 1 0 6064 [M+H]+ 419.393 6064 Found [M+H]+/[M-H]- +M424T3310 M424.4T55.2 424.399993896484 424.399993896484 424.399993896484 55.1692582034151 55.1692582034151 55.1692582034151 1 0 1 541 [M+H]+ 423.393 541 Found [M+H]+/[M-H]- +M440T4055 M440.3T67.6 440.300018310547 440.300018310547 440.300018310547 67.5889041135209 67.5725438039712 67.6052644230706 2 2 0 [M+H]+ 439.295 77 [M+H]+ 439.295 77 Found [M+H]+/[M-H]- +M441T4111 M441.1T68.5 441.100006103516 441.100006103516 441.100006103516 68.5236887576381 68.5236887576381 68.5236887576381 1 0 1 [M+K]+ 402.132 43 [M+H]+ 440.093 43 Found [M+H]+/[M-H]- +M441T4127_2 M441.1T68.8_2 441.100006103516 441.100006103516 441.100006103516 68.7816594215337 68.7816594215337 68.7816594215337 1 0 1 [M+Na]+ 418.1 23 [M+H]+ 440.093 23 Found [M+H]+/[M-H]- +M443T3159 M443T52.6 443 443 443 52.6419263083506 52.6419263083506 52.6419263083506 1 1 0 838 [M+H]+ 441.993 838 Found [M+H]+/[M-H]- +M445T4143 M444.9T69 444.899993896484 444.899993896484 444.899993896484 69.0492204926483 69.0492204926483 69.0492204926483 1 0 1 4236 [M+H]+ 443.893 4236 Found [M+H]+/[M-H]- +M446T2893 M446.2T48.2 446.200012207031 446.200012207031 446.200012207031 48.2097870775546 48.2097870775546 48.2097870775546 1 1 0 [M+Na]+ 423.211 95 [M+H]+ 445.193 95 Found [M+H]+/[M-H]- +M447T4144 M446.9T69.1 446.899993896484 446.899993896484 446.899993896484 69.0660535572266 69.0660535572266 69.0660535572266 1 0 1 5839 [M+H]+ 445.893 5839 Found [M+H]+/[M-H]- +M447T4119 M447.1T68.7 447.100006103516 447.100006103516 447.100006103516 68.6550448101035 68.6550448101035 68.6550448101035 1 0 1 120 [M+H]+ 446.093 120 Found [M+H]+/[M-H]- +M453T3745 M453.1T62.4 453.100006103516 453.100006103516 453.100006103516 62.4248546431982 62.4248546431982 62.4248546431982 1 1 0 [M+H]+ 452.1 14 [M+H]+ 452.1 14 Found [M+H]+/[M-H]- +M461T3139 M461.1T52.3 461.100006103516 461.100006103516 461.100006103516 52.3216964859304 52.3216964859304 52.3216964859304 1 0 1 [2M+Na+K-H]+ 200.089 67 [M+H]+ 460.093 67 Found [M+H]+/[M-H]- +M462T2597 M461.9T43.3 461.899993896484 461.899993896484 461.899993896484 43.2765662432725 43.2765662432725 43.2765662432725 1 1 0 2880 [M+H]+ 460.893 2880 Found [M+H]+/[M-H]- +M465T4110 M465.1T68.5 465.100006103516 465.100006103516 465.100006103516 68.4974193491718 68.4456488229912 68.4974193491718 3 0 2 [M+H-CO]+ 492.092 43 [M+H]+ 464.093 43 Found [M+H]+/[M-H]- +M469T4110 M469T68.5 469 469 469 68.4973340588448 68.4973340588448 68.4973340588448 1 0 1 43 [M+H]+ 467.993 43 Found [M+H]+/[M-H]- +M482T3312 M482.2T55.2 482.200012207031 482.200012207031 482.200012207031 55.1974320877231 55.1692582034151 55.3334338236129 3 1 2 4 [M+H]+ 481.193 4 Found [M+H]+/[M-H]- +M486T3726_2 M486T62.1_2 486 486 486 62.0950630281632 62.0578316825142 62.1322943738121 2 1 1 4683 [M+H]+ 484.993 4683 Found [M+H]+/[M-H]- +M486T3654 M486.1T60.9 486.100006103516 486.100006103516 486.100006103516 60.9050570460149 60.9050570460149 60.9050570460149 1 0 1 2410 [M+H]+ 485.093 2410 Found [M+H]+/[M-H]- +M493T2872 M493T47.9 493 493 493 47.8738616553085 47.8738616553085 47.8738616553085 1 0 1 4766 [M+H]+ 491.993 4766 Found [M+H]+/[M-H]- +M494T3069 M494.3T51.2 494.300018310547 494.300018310547 494.300018310547 51.1518080429633 51.1518080429633 51.1518080429633 1 1 0 48 [M+H]+ 493.293 48 Found [M+H]+/[M-H]- +M495T3465 M495T57.8 495 495 495 57.7519773435038 57.7519773435038 57.7519773435038 1 1 0 1283 [M+H]+ 493.993 1283 Found [M+H]+/[M-H]- +M518T3975 M518T66.3 518 518 518 66.2511083848454 66.2511083848454 66.2511083848454 1 1 0 2059 [M+H]+ 516.993 2059 Found [M+H]+/[M-H]- +M520T4132 M520.4T68.9 520.400024414062 520.400024414062 520.400024414062 68.85862190811 68.85862190811 68.85862190811 1 1 0 [M+H]+ 519.397 23 [M+H]+ 519.397 23 Found [M+H]+/[M-H]- +M522T2525 M522T42.1 522 522 522 42.0767662432725 42.0767662432725 42.0767662432725 1 1 0 [M+H]+ 520.991 5042 [M+H]+ 520.991 5042 Found [M+H]+/[M-H]- +M528T4044 M528.3T67.4 528.299987792969 528.299987792969 528.299987792969 67.3942464348878 67.3942464348878 67.3942464348878 1 0 1 106 [M+H]+ 527.293 106 Found [M+H]+/[M-H]- +M534T2893_1 M534T48.2_1 534 534 534 48.2239900144358 48.2239900144358 48.2239900144358 1 0 1 95 [M+H]+ 532.993 95 Found [M+H]+/[M-H]- +M534T3169 M534.3T52.8 534.299987792969 534.299987792969 534.299987792969 52.820858081241 52.820858081241 52.820858081241 1 1 0 791 [M+H]+ 533.293 791 Found [M+H]+/[M-H]- +M539T2671 M538.9T44.5 538.900024414062 538.900024414062 538.900024414062 44.5168831358622 44.5168831358622 44.5168831358622 1 1 0 4057 [M+H]+ 537.893 4057 Found [M+H]+/[M-H]- +M541T2916 M541.2T48.6 541.200012207031 541.200012207031 541.200012207031 48.5994804250865 48.5994804250865 48.5994804250865 1 1 0 56 [M+H]+ 540.193 56 Found [M+H]+/[M-H]- +M542T4146 M542.5T69.1 542.5 542.5 542.5 69.0919049656436 69.0919049656436 69.0919049656436 1 0 1 219 [M+H]+ 541.493 219 Found [M+H]+/[M-H]- +M545T3858 M545T64.3 545 545 545 64.2965273024001 64.2965273024001 64.2965273024001 1 1 0 1418 [M+H]+ 543.993 1418 Found [M+H]+/[M-H]- +M546T3196 M546.2T53.3 546.200012207031 546.200012207031 546.200012207031 53.2672162474893 53.2335336651218 53.3008988298567 2 1 1 [M+H]+ 545.2 30 [M+H]+ 545.2 30 Found [M+H]+/[M-H]- +M546T3373 M546.3T56.2 546.299987792969 546.299987792969 546.299987792969 56.2084220817844 56.2084220817844 56.2084220817844 1 0 1 1591 [M+H]+ 545.293 1591 Found [M+H]+/[M-H]- +M547T2882 M546.9T48 546.900024414062 546.900024414062 546.900024414062 48.0254466269442 48.0254466269442 48.0254466269442 1 1 0 131 [M+H]+ 545.893 131 Found [M+H]+/[M-H]- +M547T2930 M546.9T48.8 546.900024414062 546.900024414062 546.900024414062 48.8327454465577 48.8327454465577 48.8327454465577 1 0 1 3632 [M+H]+ 545.893 3632 Found [M+H]+/[M-H]- +M548T4180_2 M548.1T69.7_2 548.100036621094 548.100036621094 548.100036621094 69.6686714714612 69.6686714714612 69.6686714714612 1 1 0 6024 [M+H]+ 547.093 6024 Found [M+H]+/[M-H]- +M551T3507 M551.1T58.5 551.100036621094 551.100036621094 551.100036621094 58.452956891696 58.452956891696 58.452956891696 1 1 0 76 [M+H]+ 550.093 76 Found [M+H]+/[M-H]- +M552T3631 M552.3T60.5 552.299987792969 552.299987792969 552.299987792969 60.5122878429917 60.5122878429917 60.5122878429917 1 0 1 2359 [M+H]+ 551.293 2359 Found [M+H]+/[M-H]- +M552T3836 M552.4T63.9 552.400024414062 552.400024414062 552.400024414062 63.9252990982341 63.9252990982341 63.9252990982341 1 0 1 3360 [M+H]+ 551.393 3360 Found [M+H]+/[M-H]- +M552T2806 M552.5T46.8 552.5 552.5 552.5 46.7628430062386 46.7628430062386 46.7628430062386 1 0 1 154 [M+H]+ 551.493 154 Found [M+H]+/[M-H]- +M555T2628 M554.8T43.8 554.799987792969 554.799987792969 554.799987792969 43.800633744761 43.800633744761 43.800633744761 1 1 0 2677 [M+H]+ 553.793 2677 Found [M+H]+/[M-H]- +M560T3524 M560.1T58.7 560.100036621094 560.100036621094 560.100036621094 58.7409233247563 58.7409233247563 58.7409233247563 1 1 0 363 [M+H]+ 559.093 363 Found [M+H]+/[M-H]- +M561T3500 M560.9T58.3 560.900024414062 560.900024414062 560.900024414062 58.3265122292451 58.3265122292451 58.3265122292451 1 0 1 3396 [M+H]+ 559.893 3396 Found [M+H]+/[M-H]- +M566T2712 M566T45.2 566 566 566 45.2077855778326 45.2077855778326 45.2077855778326 1 1 0 2531 [M+H]+ 564.993 2531 Found [M+H]+/[M-H]- +M567T2630 M566.8T43.8 566.799987792969 566.799987792969 566.799987792969 43.8272182117096 43.8272182117096 43.8272182117096 1 1 0 2685 [M+H]+ 565.793 2685 Found [M+H]+/[M-H]- +M570T3689 M570.5T61.5 570.5 570.5 570.5 61.4882293714724 61.4882293714724 61.4882293714724 1 0 1 617 [M+H]+ 569.493 617 Found [M+H]+/[M-H]- +M572T2893 M571.6T48.2 571.600036621094 571.600036621094 571.600036621094 48.2097870775546 48.2097870775546 48.2097870775546 1 1 0 95 [M+H]+ 570.593 95 Found [M+H]+/[M-H]- +M574T2913 M573.7T48.5 573.700012207031 573.700012207031 573.700012207031 48.5481814919484 48.5481814919484 48.5481814919484 1 1 0 [M+H]+ 572.692 56 [M+H]+ 572.692 56 Found [M+H]+/[M-H]- +M575T2527 M574.7T42.1 574.700012207031 574.700012207031 574.700012207031 42.1194514146668 42.1194514146668 42.1194514146668 1 0 1 5962 [M+H]+ 573.693 5962 Found [M+H]+/[M-H]- +M578T2852 M578.3T47.5 578.299987792969 578.299987792969 578.299987792969 47.5401992175178 47.4984694680838 47.5819289669518 2 1 1 111 [M+H]+ 577.293 111 Found [M+H]+/[M-H]- +M578T3834 M578.4T63.9 578.400024414062 578.400024414062 578.400024414062 63.903380773541 63.903380773541 63.903380773541 1 1 0 3346 [M+H]+ 577.393 3346 Found [M+H]+/[M-H]- +M580T3296 M579.5T54.9 579.5 579.5 579.5 54.9340092491062 54.9340092491062 54.9340092491062 1 1 0 2610 [M+H]+ 578.493 2610 Found [M+H]+/[M-H]- +M582T3848_2 M582.5T64.1_2 582.5 582.5 582.5 64.1317421799532 64.1317421799532 64.1317421799532 1 1 0 [M+H]+ 581.493 21 [M+H]+ 581.493 21 Found [M+H]+/[M-H]- +M583T3496 M583T58.3 583 583 583 58.2713130322852 58.2713130322852 58.2713130322852 1 1 0 3516 [M+H]+ 581.993 3516 Found [M+H]+/[M-H]- +M583T2581 M583.4T43 583.400024414062 583.400024414062 583.400024414062 43.0206214460137 43.0206214460137 43.0206214460137 1 1 0 5692 [M+H]+ 582.393 5692 Found [M+H]+/[M-H]- +M584T2539 M584.4T42.3 584.400024414062 584.400024414062 584.400024414062 42.3115162432725 42.3115162432725 42.3115162432725 1 1 0 5558 [M+H]+ 583.393 5558 Found [M+H]+/[M-H]- +M586T2762 M585.9T46 585.900024414062 585.900024414062 585.900024414062 46.0265819700675 46.0265819700675 46.0265819700675 1 1 0 94 [M+H]+ 584.893 94 Found [M+H]+/[M-H]- +M592T4176 M591.5T69.6 591.5 591.5 591.5 69.5927325930257 69.5927325930257 69.5927325930257 1 1 0 115 [M+H]+ 590.493 115 Found [M+H]+/[M-H]- +M593T3448 M593.3T57.5 593.299987792969 593.299987792969 593.299987792969 57.4737949279535 57.4737949279535 57.4737949279535 1 0 1 2939 [M+H]+ 592.293 2939 Found [M+H]+/[M-H]- +M596T4172 M596.1T69.5 596.100036621094 596.100036621094 596.100036621094 69.5403852759756 69.5403852759756 69.5403852759756 1 1 0 4425 [M+H]+ 595.093 4425 Found [M+H]+/[M-H]- +M597T2724 M596.8T45.4 596.799987792969 596.799987792969 596.799987792969 45.3955462015806 45.3955462015806 45.3955462015806 1 0 1 2540 [M+H]+ 595.793 2540 Found [M+H]+/[M-H]- +M598T2738 M597.8T45.6 597.799987792969 597.799987792969 597.799987792969 45.628120700158 45.628120700158 45.628120700158 1 0 1 4444 [M+H]+ 596.793 4444 Found [M+H]+/[M-H]- +M598T3811 M598.3T63.5 598.299987792969 598.299987792969 598.299987792969 63.5166230732481 63.5166230732481 63.5166230732481 1 1 0 46 [M+H]+ 597.293 46 Found [M+H]+/[M-H]- +M598T3177 M598.5T52.9 598.5 598.5 598.5 52.947766074638 52.947766074638 52.947766074638 1 1 0 801 [M+H]+ 597.493 801 Found [M+H]+/[M-H]-