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(-) [+]
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--- /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
Binary file static/images/combinexsannos_variableMetadata.png has changed
Binary file static/images/combinexsannos_workflow.png has changed
Binary file static/images/combinexsannos_workflow_zoom.png has changed
Binary file test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata has changed
Binary file test-data/faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata has changed
--- /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]-