Mercurial > repos > lecorguille > camera_annotate
changeset 13:1c30ff90f3ae draft
planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
author | lecorguille |
---|---|
date | Fri, 07 Apr 2017 07:42:18 -0400 |
parents | 9c037181588e |
children | 225cb8347572 |
files | CAMERA.r README.rst abims_CAMERA_annotateDiffreport.xml lib.r macros.xml static/images/annotate_workflow.png test-data/CASMI_extended_NEG_rules.csv test-data/CASMI_extended_POS_rules.csv test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv test-data/ko15.CDF test-data/ko16.CDF test-data/wt15.CDF test-data/wt16.CDF tool_dependencies.xml |
diffstat | 18 files changed, 25652 insertions(+), 8679 deletions(-) [+] |
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--- a/CAMERA.r Wed Feb 01 12:24:04 2017 -0500 +++ b/CAMERA.r Fri Apr 07 07:42:18 2017 -0400 @@ -11,12 +11,12 @@ #pkgs=c("xcms","batch") pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch") for(p in pkgs) { - suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) - cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") + suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") } source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } -cat("\n\n"); +cat("\n\n"); @@ -34,25 +34,25 @@ #image is an .RData file necessary to use xset variable given by previous tools if (!is.null(listArguments[["image"]])){ - load(listArguments[["image"]]); listArguments[["image"]]=NULL + load(listArguments[["image"]]); listArguments[["image"]]=NULL } if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) { - load(listArguments[["image_pos"]]) - xaP=xa - listOFlistArgumentsP=listOFlistArguments - if (exists("xsAnnotate_object")) xaP=xsAnnotate_object - - diffrepP=NULL - if (exists("diffrep")) diffrepP=diffrep + load(listArguments[["image_pos"]]) + xaP=xa + listOFlistArgumentsP=listOFlistArguments + if (exists("xsAnnotate_object")) xaP=xsAnnotate_object + + diffrepP=NULL + if (exists("diffrep")) diffrepP=diffrep - load(listArguments[["image_neg"]]) - xaN=xa - listOFlistArgumentsN=listOFlistArguments - if (exists("xsAnnotate_object")) xaN=xsAnnotate_object + load(listArguments[["image_neg"]]) + xaN=xa + listOFlistArgumentsN=listOFlistArguments + if (exists("xsAnnotate_object")) xaN=xsAnnotate_object - diffrepN=NULL - if (exists("diffrep")) diffrepN=diffrep + diffrepN=NULL + if (exists("diffrep")) diffrepN=diffrep } @@ -73,67 +73,42 @@ xsetRdataOutput = paste(thefunction,"RData",sep=".") if (!is.null(listArguments[["xsetRdataOutput"]])){ - xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL + xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL } rplotspdf = "Rplots.pdf" if (!is.null(listArguments[["rplotspdf"]])){ - rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL + rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL } dataMatrixOutput = "dataMatrix.tsv" if (!is.null(listArguments[["dataMatrixOutput"]])){ - dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL + dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL } variableMetadataOutput = "variableMetadata.tsv" if (!is.null(listArguments[["variableMetadataOutput"]])){ - variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL -} - -if (!is.null(listArguments[["new_file_path"]])){ - new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL + variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL } #Import the different functions source_local("lib.r") -#necessary to unzip .zip file uploaded to Galaxy -#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories - - -if (!is.null(listArguments[["zipfile"]])){ - zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL -} - # We unzip automatically the chromatograms from the zip files. if (thefunction %in% c("annotatediff")) { - if(exists("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) - } - - #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") - } + if (!exists("zipfile")) zipfile=NULL + if (!exists("singlefile")) singlefile=NULL + rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) + zipfile = rawFilePath$zipfile + singlefile = rawFilePath$singlefile + listArguments = rawFilePath$listArguments + directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) } - #addition of xset object to the list of arguments in the first position if (exists("xset") != 0){ - listArguments=append(list(xset), listArguments) + listArguments=append(list(xset), listArguments) } cat("\n\n") @@ -149,25 +124,32 @@ if (thefunction %in% c("annotatediff")) { - results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path) - xa=results_list[["xa"]] - diffrep=results_list[["diffrep"]] - variableMetadata=results_list[["variableMetadata"]] + results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput) + xa=results_list[["xa"]] + diffrep=results_list[["diffrep"]] + variableMetadata=results_list[["variableMetadata"]] - cat("\n\n") - cat("\tXSET OBJECT INFO\n") - print(xa) + cat("\n\n") + cat("\tXSET OBJECT INFO\n") + print(xa) } if (thefunction %in% c("combinexsAnnos")) { - cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput) + cAnnot=combinexsAnnos_function( + xaP=xaP,xaN=xaN, + listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN, + diffrepP=diffrepP,diffrepN=diffrepN, + pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]], + convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]], + variableMetadataOutput=variableMetadataOutput + ) } dev.off() #saving R data in .Rdata file to save the variables used in the present tool -objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile") +objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile","singlefile") save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) cat("\n\n")
--- a/README.rst Wed Feb 01 12:24:04 2017 -0500 +++ b/README.rst Fri Apr 07 07:42:18 2017 -0400 @@ -2,6 +2,21 @@ Changelog/News -------------- +**Version 2.2.0 - 03/02/2017** + +- BUGFIX: the diffreport ids didn't convert the rt in minute as the other export + +- UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata. + +- IMPROVEMENT: add some sections within the form to separate the different parts of the process + +- IMPROVEMENT: add the possibility to use defined ruleset + +- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants + +- IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet + + **Version 2.1.5 - 21/04/2016** - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 @@ -22,26 +37,15 @@ - UPDATE: refactoring of internal management of inputs/outputs -VERSION 2.1.0 - 09/10/2015** +**VERSION 2.1.0 - 09/10/2015** - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) -VERSION 2.1.0 - 07/06/2015** +**VERSION 2.1.0 - 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. - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions - - - -Test Status ------------ - -Planemo test using conda: passed - -Planemo test using source env.sh: passed - -Planemo shed_test : passed
--- a/abims_CAMERA_annotateDiffreport.xml Wed Feb 01 12:24:04 2017 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Fri Apr 07 07:42:18 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.0"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> - + <macros> <import>macros.xml</import> </macros> @@ -11,213 +11,225 @@ <command><![CDATA[ @COMMAND_CAMERA_SCRIPT@ - xfunction annotatediff - image $image + xfunction annotatediff + image '$image' - variableMetadataOutput $variableMetadata - dataMatrixOutput $datamatrix - xsetRdataOutput $rdata - - convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1} - sigma $sigma perfwhm $perfwhm - maxcharge $maxcharge maxiso $maxiso minfrac $minfrac - ppm $ppm mzabs $mzabs intval $intval - max_peaks $max_peaks + + ## output + variableMetadataOutput '$variableMetadata' + dataMatrixOutput '$datamatrix' + + ## groupFWHM + sigma $groupfwhm.sigma + perfwhm $groupfwhm.perfwhm + + ## findGeneral + ppm $findgeneral.ppm + mzabs $findgeneral.mzabs + + ## findIsotopes + maxcharge $findisotopes.maxcharge + maxiso $findisotopes.maxiso + minfrac $findisotopes.minfrac + quick $quick_block.quick - #if $quick_block.quick == "FALSE" - polarity $quick_block.polarity - cor_eic_th $quick_block.cor_eic_th - graphMethod $quick_block.graphMethod - pval $quick_block.pval - calcCiS $quick_block.calcCiS - calcIso $quick_block.calcIso - calcCaS $quick_block.calcCaS - multiplier $quick_block.multiplier + #if $quick_block.quick == "FALSE": + xsetRdataOutput '$rdata_quick_false' + + ## groupcorr + cor_eic_th $quick_block.groupcorr.cor_eic_th + graphMethod $quick_block.groupcorr.graphMethod + pval $quick_block.groupcorr.pval + calcCiS $quick_block.groupcorr.calcCiS + calcIso $quick_block.groupcorr.calcIso + calcCaS $quick_block.groupcorr.calcCaS + + ## findadducts + polarity $quick_block.findadducts.polarity + max_peaks $quick_block.findadducts.max_peaks + #if $quick_block.findadducts.rules_block.rules_select == "FALSE": + multiplier $quick_block.findadducts.rules_block.multiplier + #else + rules $quick_block.findadducts.rules_block.rules + #end if + #else + xsetRdataOutput '$rdata_quick_true' #end if - #if $options.option == "show": + #if $diffreport.options.option == "show": + ## diffreport runDiffreport TRUE - eicmax $options.eicmax - eicwidth $options.eicwidth - value $options.value - sortpval $options.sortpval - h $options.h - w $options.w - mzdec $options.mzdec - new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ + eicmax $diffreport.options.eicmax + eicwidth $diffreport.options.eicwidth + value $diffreport.options.value + sortpval $diffreport.options.sortpval + h $diffreport.options.h + w $diffreport.options.w + mzdec $diffreport.options.mzdec #end if - - @COMMAND_ZIPFILE_LOAD@ + + @COMMAND_PEAKLIST@ + + @COMMAND_FILE_LOAD@ ]]></command> <inputs> - - + + <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" /> - <param name="convert_param" 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="num_digits" type="integer" value="4" label="" help="Number of decimal places for mass values reported in ions identifiers. A minimum of 4 decimal places should be set" /> + <section name="groupfwhm" title="Group co-eluted peaks based on RT [groupFWHM]" expanded="True"> + <param name="sigma" type="integer" value="6" label="Multiplier of the standard deviation" help="[sigma]" /> + <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="Percentage of FWHM width" help="[perfwhm]" /> + </section> + + <section name="findgeneral" title="Annotation general options" expanded="True"> + <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" /> + <param name="mzabs" type="float" value="0.015" label="General absolut error in m/z" help="[mzabs]" /> + </section> - <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" /> - <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" /> - <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" /> - <param name="maxiso" type="integer" value="4" label="findIsotopes: max. number of expected isotopes" help="[maxiso]" /> - <param name="minfrac" type="float" value="0.5" max="1" min="0" label="findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" /> - <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" /> - <param name="mzabs" type="float" value="0.015" label="mzabs" help="General absolut error in m/z" /> - <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 name="findisotopes" title="Annotate Isotopes [findIsotopes]" expanded="True"> + <param name="maxcharge" type="integer" value="3" label="Max. ion charge" help="[maxcharge]" /> + <param name="maxiso" type="integer" value="4" label="Max. number of expected isotopes" help="[maxiso]" /> + <param name="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" /> + </section> - <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" /> <conditional name="quick_block"> - <param name="quick" type="select" label="Quick mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts"> - <option value="TRUE">TRUE</option> - <option value="FALSE" selected="true">FALSE</option> + <param name="quick" type="select" label="Mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts"> + <option value="FALSE" selected="true">All functions</option> + <option value="TRUE">Only groupFWHM and findIsotopes functions [quick]</option> </param> <when value="FALSE"> - <param name="polarity" type="select" label="findAdducts: Which polarity mode was used for measuring of the ms sample" help="polarity"> - <option value="positive" >positive</option> - <option value="negative" selected="true">negative</option> - </param> - <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" /> - <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]"> - <option value="hcs" selected="true">hcs</option> - <option value="lpc">lpc</option> - </param> - <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" /> - <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/> - <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/> - <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/> - <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> - </when> - <when value="TRUE"> + + <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]" expanded="True"> + <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" /> + <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]"> + <option value="hcs" selected="true">hcs</option> + <option value="lpc">lpc</option> + </param> + <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" /> + <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/> + <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/> + <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/> + </section> + + <section name="findadducts" title="Annotate Adducts [findAdducts]" expanded="True"> + <param name="polarity" type="select" label="Which polarity mode was used for measuring of the ms sample" help="polarity"> + <option value="positive" >positive</option> + <option value="negative" selected="true">negative</option> + </param> + <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" /> + <conditional name="rules_block"> + <param name="rules_select" type="select" label="Use a personal ruleset file"> + <option value="TRUE">TRUE</option> + <option value="FALSE" selected="true">FALSE</option> + </param> + <when value="FALSE"> + <param name="multiplier" type="integer" value="3" label="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> + </when> + <when value="TRUE"> + <param name="rules" type="data" format="csv" label="User defined ruleset" help="[rules]" /> + </when> + </conditional> + </section> + + </when> + <when value="TRUE"> <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" /> - </when> - </conditional> - - - <!-- Annotatediffreport specific parameters --> - <conditional name="options"> - <param name="option" type="select" label="Number of condition"> - <option value="hide" selected="true">One condition</option> - <option value="show">Two or more conditions</option> - </param> - <when value="show"> - <param name="eicmax" type="integer" value="0" label="diffreport: number of the most significantly different analytes to create EICs for" help="[eicmax]" /> - <param name="eicwidth" type="integer" value="200" label="diffreport: width (in seconds) of EICs produced" help="[eicwidth]" /> - <param name="value" type="select" label="diffreport: Intensity values to be used for the diffreport" help="[value]"> - <option value="into" selected="true">into</option> - <option value="maxo" >maxo</option> - <option value="intb">intb</option> - </param> - <param name="h" type="integer" value="480" label="diffreport: Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" /> - <param name="w" type="integer" value="640" label="diffreport: Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> - <param name="mzdec" type="integer" value="2" label="diffreport: Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> - <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="diffreport: logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> - </when> - <when value="hide"> </when> </conditional> - - <expand macro="zipfile_load"/> + + <!-- Diffreport specific parameters --> + <section name="diffreport" title="Statistics and results export: [diffreport]" expanded="True"> + <conditional name="options"> + <param name="option" type="select" label="Number of condition"> + <option value="hide" selected="true">One condition</option> + <option value="show">Two or more conditions</option> + </param> + <when value="show"> + <param name="eicmax" type="integer" value="0" label="Number of the most significantly different analytes to create EICs for" help="[eicmax]" /> + <param name="eicwidth" type="integer" value="200" label="Width (in seconds) of EICs produced" help="[eicwidth]" /> + <param name="value" type="select" label="Intensity values to be used for the diffreport" help="[value]"> + <option value="into" selected="true">into</option> + <option value="maxo" >maxo</option> + <option value="intb">intb</option> + </param> + <param name="h" type="integer" value="480" label="Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" /> + <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> + <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> + <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> + </when> + <when value="hide"> + </when> + </conditional> + </section> + + <expand macro="input_peaklist"/> + <expand macro="input_file_load"/> </inputs> <outputs> <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> - <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" > + <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" > + <filter>quick_block['quick'] == 'FALSE'</filter> <change_format> - <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> - <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> + <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" /> + <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" /> </change_format> </data> - <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> - <filter>(options['option'] == 'show')</filter> - </data> + <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" > + <filter>quick_block['quick'] == 'TRUE'</filter> + </data> + <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true"> + <filter>diffreport['options']['option'] == 'show'</filter> + <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" /> + <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" /> + </data> </outputs> - + <tests> - <!--<test> - <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/> - <param name="convert_param" value="False"/> - <param name="num_digits" value="0"/> - <param name="sigma" value="6"/> - <param name="perfwhm" value="0.6"/> - <param name="maxcharge" value="3"/> - <param name="maxiso" value="4"/> - <param name="minfrac" value="0.5"/> - <param name="ppm" value="5"/> - <param name="mzabs" value="0.015"/> - <param name="intval" value="into"/> - <param name="max_peaks" value="100"/> - <param name="quick_block|quick" value="FALSE"/> - <param name="quick_block|polarity" value="negative"/> - <param name="quick_block|cor_eic_th" value="0.75"/> - <param name="quick_block|graphMethod" value="hcs"/> - <param name="quick_block|pval" value="0.05"/> - <param name="quick_block|calcCiS" value="True"/> - <param name="quick_block|calcIso" value="False"/> - <param name="quick_block|calcCaS" value="False"/> - <param name="quick_block|multiplier" value="3"/> - <param name="options|option" value="show"/> - <param name="options|eicmax" value="200"/> - <param name="options|eicwidth" value="200"/> - <param name="options|value" value="into"/> - <param name="options|h" value="480"/> - <param name="options|w" value="640"/> - <param name="options|mzdec" value="2"/> - <param name="options|sortpval" value="False"/> - <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> - <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> - <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> - </test>--> <test> <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> - <param name="convert_param" value="False"/> - <param name="num_digits" value="0"/> - <param name="sigma" value="6"/> - <param name="perfwhm" value="0.6"/> - <param name="maxcharge" value="3"/> - <param name="maxiso" value="4"/> - <param name="minfrac" value="0.5"/> - <param name="ppm" value="5"/> - <param name="mzabs" value="0.015"/> - <param name="intval" value="into"/> - <param name="max_peaks" value="100"/> - <param name="quick_block|quick" value="FALSE"/> - <param name="quick_block|polarity" value="negative"/> - <param name="quick_block|cor_eic_th" value="0.75"/> - <param name="quick_block|graphMethod" value="hcs"/> - <param name="quick_block|pval" value="0.05"/> - <param name="quick_block|calcCiS" value="True"/> - <param name="quick_block|calcIso" value="False"/> - <param name="quick_block|calcCaS" value="False"/> - <param name="quick_block|multiplier" value="3"/> - <param name="options|option" value="show"/> - <param name="options|eicmax" value="200"/> - <param name="options|eicwidth" value="200"/> - <param name="options|value" value="into"/> - <param name="options|h" value="480"/> - <param name="options|w" value="640"/> - <param name="options|mzdec" value="2"/> - <param name="options|sortpval" value="False"/> - <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> - <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <expand macro="test_annotate_diffreport"/> + <expand macro="test_annotate_quick_true"/> + <expand macro="test_file_load_zip"/> <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> </test> + <test> + <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> + <expand macro="test_annotate_diffreport"/> + <expand macro="test_annotate_quick_true"/> + <expand macro="test_file_load_single"/> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> + <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> + </test> + <test> + <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> + <expand macro="test_annotate_diffreport"/> + <conditional name="quick_block"> + <expand macro="test_annotate_quick_false" /> + <section name="findadducts"> + <param name="polarity" value="negative"/> + <conditional name="rules_block"> + <param name="rules_select" value="TRUE"/> + <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/> + </conditional> + </section> + </conditional> + <expand macro="test_file_load_single"/> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" /> + <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" /> + </test> </tests> - - - + + + <help><![CDATA[ - + @HELP_AUTHORS@ ================ @@ -239,7 +251,7 @@ **What it does?** -The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable). +The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable). If you have two or more conditions, it will return a diffreport result within the annotation results. The diffreport result shows the most significant differences between two sets of samples. Optionally @@ -265,7 +277,7 @@ +---------------------------+---------------------------------------+------------------------------------------------+ | Name | Output file | Format | +===========================+=======================================+================================================+ -|CAMERA_combinexsAnnot |xset.annotate.dataMatrix.tsv | rdata.camera.positive or rdata.camera.negative | +|CAMERA_combinexsAnnot |xset.annotate.Rdata | rdata.camera.positive or rdata.camera.negative | +---------------------------+---------------------------------------+------------------------------------------------+ |Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular | +---------------------------+---------------------------------------+------------------------------------------------+ @@ -303,6 +315,22 @@ +---------------------------+---------------------------+ +[Optional] User defined ruleset: +-------------------------------- + +Example: + + | "name","nmol","charge","massdiff","oidscore","quasi","ips" + | "[M-H]-",1,-1,-1.007276,1,1,1 + | "[M-2H]2-",1,-2,-2.014552,2,0,1 + | "[M-3H]3-",1,-3,-3.021828,3,0,1 + | "[M-2H+Na]-",1,-1,20.974666,4,0,0.25 + | "[M-H+Cl]2-",1,-2,33.962126,5,0,1 + | "[M-2H+K]-",1,-1,36.948606,6,0,0.25 + | "[M+Cl]-",1,-1,34.969402,7,1,1 + | "[M+2Cl]2-",1,-2,69.938804,8,0,1 + | "[2M-H]-",2,-1,-1.007276,1,0,0.5 + ---------- Parameters ---------- @@ -328,7 +356,7 @@ xset.annotate.dataMatrix.tsv | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column). - + xset.annotate.zip | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis). @@ -336,10 +364,10 @@ xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative | Rdata file, that be used outside Galaxy in R. - + ------ -.. class:: infomark +.. class:: infomark The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow: @@ -349,7 +377,7 @@ | PCA (Statistical analysis) | Hierarchical Clustering (Statistical analysis) - + --------------------------------------------------- --------------- @@ -377,7 +405,7 @@ | eicmax -> **200** | eicwidth -> **200 (default)** - + Output files ------------ @@ -386,7 +414,7 @@ .. image:: annotatediffreport_dataMatrix.png -**Example of a part of xset.annotate.variableMetadata.tsv output** +**Example of a part of xset.annotate.variableMetadata.tsv output** .. image:: annotatediffreport_variableMetadata.png @@ -396,9 +424,24 @@ Changelog/News -------------- +**Version 2.2.0 - 28/03/2017** + +- BUGFIX: the diffreport ids didn't convert the rt in minute as the other export + +- UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata. + +- IMPROVEMENT: add some sections within to separate the different parts of the process + +- IMPROVEMENT: add the possibility to use defined ruleset + +- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants + +- IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet + + **Version 2.1.5 - 21/04/2016** -- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 +- UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0 **Version 2.1.4 - 18/04/2016** @@ -417,12 +460,12 @@ - UPDATE: refactoring of internal management of inputs/outputs -VERSION 2.1.0 - 09/10/2015** +**VERSION 2.1.0 - 09/10/2015** - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) -VERSION 2.1.0 - 07/06/2015** +**VERSION 2.1.0 - 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. @@ -437,5 +480,3 @@ </tool> - -
--- a/lib.r Wed Feb 01 12:24:04 2017 -0500 +++ b/lib.r Fri Apr 07 07:42:18 2017 -0400 @@ -1,188 +1,304 @@ -# lib.r version="2.2.1" +# lib.r + +#@author G. Le Corguille +#The function create a pdf from the different png generated by diffreport +diffreport_png2pdf <- function(filebase) { + dir.create("pdf") -#The function create a pdf from the different png generated by diffreport -diffreport_png2pdf <- function(filebase, new_file_path) { + 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)) + +} - pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="") - pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="") +#@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) +} - system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep="")) - system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep="")) - - file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput) - file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput) +#@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, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) { - # 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 ------- - listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]]) - listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]]) - listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]]) +annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv") { + # Resolve the bug with x11, with the function png + options(bitmapType='cairo') - #graphMethod parameter bugs where this parameter is not defined in quick=true - if(listArguments[["quick"]]==TRUE) { - xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]]) - } - else { - xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]],multiplier=listArguments[["multiplier"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]]) - - } - peakList=getPeaklist(xa,intval=listArguments[["intval"]]) - peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); - - - # --- Multi condition : diffreport --- - diffrep=NULL - if (!is.null(listArguments[["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-") + + # ------ annot ------- + listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]]) + listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]]) + listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]]) - diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]]) - #combines results - diffreportTSV=merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F) - diffreportTSV=cbind(diffreportTSV[,!(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))],diffreportTSV[,(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))]) + # common parameters + listArguments4annotate = list(object=xset, + nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]], + maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]], + ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]], + polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]]) - if(listArguments[["sortpval"]]){ - diffreportTSV=diffreportTSV[order(diffreportTSV$pvalue), ] - } - - if (listArguments[["convert_param"]]){ - #converting the retention times (seconds) into minutes - diffreportTSV$rt=diffreportTSV$rt/60;diffreportTSV$rtmin=diffreportTSV$rtmin/60; diffreportTSV$rtmax=diffreportTSV$rtmax/60; - } - write.table(diffreportTSV, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep="")) + # quick == FALSE + if(listArguments[["quick"]]==FALSE) { + listArguments4annotate = append(listArguments4annotate, + list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]], + calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]])) + # no ruleset + if (!is.null(listArguments[["multiplier"]])) { + listArguments4annotate = append(listArguments4annotate, + list(multiplier=listArguments[["multiplier"]])) + } + # ruleset + else { + rulset=read.table(listArguments[["rules"]], h=T, sep=";") + if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep="\t") + if (ncol(rulset) < 4) rulset=read.table(listArguments[["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) + } - if (listArguments[["eicmax"]] != 0) { - diffreport_png2pdf(filebase, new_file_path) - } + listArguments4annotate = append(listArguments4annotate, + list(rules=rulset)) } - } } - } + # launch annotate + xa = do.call("annotate", listArguments4annotate) + peakList=getPeaklist(xa,intval=listArguments[["intval"]]) + peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); + + # --- dataMatrix --- + dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c("name", make.names(sampnames(xa@xcmsSet))))] + write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput) - # --- variableMetadata --- - variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] - # if we have 2 conditions, we keep stat of diffrep - if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) { - variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F) - if(exists("listArguments[[\"sortpval\"]]")){ - variableMetadata=variableMetadata[order(variableMetadata$pvalue), ] + # --- Multi condition : diffreport --- + diffrepOri=NULL + if (!is.null(listArguments[["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=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]]) + + 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, listArguments[["convertRTMinute"]]) + diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]]) + + if(listArguments[["sortpval"]]){ + diffrep=diffrep[order(diffrep$pvalue), ] + } + + dir.create("tabular") + write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep="")) + + if (listArguments[["eicmax"]] != 0) { + diffreport_png2pdf(filebase) + } + } + } + } } - } - variableMetadataOri=variableMetadata - if (listArguments[["convert_param"]]){ - #converting the retention times (seconds) into minutes - print("converting the retention times into minutes in the variableMetadata") - variableMetadata$rt=variableMetadata$rt/60;variableMetadata$rtmin=variableMetadata$rtmin/60; variableMetadata$rtmax=variableMetadata$rtmax/60; - } - #Transform metabolites name - variableMetadata$name= paste("M",round(variableMetadata$mz,digits=listArguments[["num_digits"]]),"T",round(variableMetadata$rt),sep="") - write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) - # --- dataMatrix --- - dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] - dataMatrix=cbind(peakList$name,dataMatrix); colnames(dataMatrix)[1] = c("name"); + # --- variableMetadata --- + variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] + variableMetadata = RTSecondToMinute(variableMetadata, listArguments[["convertRTMinute"]]) + variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]]) + # if we have 2 conditions, we keep stat of diffrep + if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) { + variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F) + if(exists("listArguments[[\"sortpval\"]]")){ + variableMetadata=variableMetadata[order(variableMetadata$pvalue), ] + } + } - if (listArguments[["convert_param"]]){ - #converting the retention times (seconds) into minutes - print("converting the retention times into minutes in the dataMatrix ids") - peakList$rt=peakList$rt/60 - } - dataMatrix$name= paste("M",round(peakList$mz,digits=listArguments[["num_digits"]]),"T",round(peakList$rt),sep="") - write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput) - - return(list("xa"=xa,"diffrep"=diffrep,"variableMetadata"=variableMetadataOri)); + 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, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){ +combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, 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") + #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("\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.") - } - - + 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 - listOFlistArgumentsP=listOFlistArguments - mode="neg. Mode" - } else { - xa=xaN - listOFlistArgumentsN=listOFlistArguments - mode="pos. Mode" - } - intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval } - peakList=getPeaklist(xa,intval=intval) - 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)))] + if(pos){ + xa=xaP + listOFlistArgumentsP=listOFlistArguments + mode="neg. Mode" + } else { + xa=xaN + listOFlistArgumentsN=listOFlistArguments + 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="") - #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 = 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"); - #If the user want to convert the retention times (seconds) into minutes. - if (listArguments[["convert_param"]]){ - #converting the retention times (seconds) into minutes - cat("\tConverting the retention times into minutes\n") - variableMetadata$rtmed=cAnnot$rt/60; variableMetadata$rtmin=cAnnot$rtmin/60; variableMetadata$rtmax=cAnnot$rtmax/60; - } + 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); + #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, listArguments) { + if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]] + if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]] + if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]] + + if (!is.null(listArguments[["singlefile_galaxyPath"]])) { + singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]]; + singlefile_sampleNames = listArguments[["singlefile_sampleName"]] + } + if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) { + singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]]; + singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]] + } + if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) { + singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]]; + singlefile_sampleNames = listArguments[["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")) { + listArguments[[argument]]=NULL + } + return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments)) +} + + +# 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) +}
--- a/macros.xml Wed Feb 01 12:24:04 2017 -0500 +++ b/macros.xml Fri Apr 07 07:42:18 2017 -0400 @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="0.4_1">r-snow</requirement> <requirement type="package" version="1.26.0">bioconductor-camera</requirement> <requirement type="package" version="2.26.0">bioconductor-multtest</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="1.6.27">libpng</requirement> - <requirement type="package" version="1.3.20">graphicsmagick</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.3.23">graphicsmagick</requirement> </requirements> </xml> <xml name="stdio"> @@ -19,33 +18,137 @@ <token name="@COMMAND_CAMERA_SCRIPT@"> LANG=C Rscript $__tool_directory__/CAMERA.r </token> - - <!-- zipfile load for planemo test --> - <token name="@COMMAND_ZIPFILE_LOAD@"> - #if $zipfile_load_conditional.zipfile_load_select == "yes": - #if $zipfile_load_conditional.zip_file: - zipfile $zipfile_load_conditional.zip_file + + <!-- 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 + #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="zipfile_load"> - <conditional name="zipfile_load_conditional"> - <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes" selected="peakgroups">yes</option> + + <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> - <when value="no"> - </when> - <when value="yes"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> + </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 +**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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CASMI_extended_NEG_rules.csv Fri Apr 07 07:42:18 2017 -0400 @@ -0,0 +1,111 @@ +"name","nmol","charge","massdiff","oidscore","quasi","ips" +"[M-H]-",1,-1,-1.007276,1,1,1 +"[M-2H]2-",1,-2,-2.014552,2,0,1 +"[M-3H]3-",1,-3,-3.021828,3,0,1 +"[M-2H+Na]-",1,-1,20.974666,4,0,0.25 +"[M-H+Cl]2-",1,-2,33.962126,5,0,1 +"[M-2H+K]-",1,-1,36.948606,6,0,0.25 +"[M+Cl]-",1,-1,34.969402,7,1,1 +"[M+2Cl]2-",1,-2,69.938804,8,0,1 +"[2M-H]-",2,-1,-1.007276,1,0,0.5 +"[2M-2H]2-",2,-2,-2.014552,2,0,0.5 +"[2M-3H]3-",2,-3,-3.021828,3,0,0.5 +"[2M-2H+Na]-",2,-1,20.974666,4,0,0.25 +"[2M-H+Cl]2-",2,-2,33.962126,5,0,0.5 +"[2M-2H+K]-",2,-1,36.948606,6,0,0.25 +"[2M+Cl]-",2,-1,34.969402,7,0,0.5 +"[2M+2Cl]2-",2,-2,69.938804,8,0,0.5 +"[3M-H]-",3,-1,-1.007276,1,0,0.5 +"[3M-2H]2-",3,-2,-2.014552,2,0,0.5 +"[3M-3H]3-",3,-3,-3.021828,3,0,0.5 +"[3M-2H+Na]-",3,-1,20.974666,4,0,0.25 +"[3M-H+Cl]2-",3,-2,33.962126,5,0,0.5 +"[3M-2H+K]-",3,-1,36.948606,6,0,0.25 +"[3M+Cl]-",3,-1,34.969402,7,0,0.5 +"[3M+2Cl]2-",3,-2,69.938804,8,0,0.5 +"[M+Cl+NaCOOH]-",1,-1,102.956842,9,0,0.5 +"[M-H+NaCOOH]-",1,-1,66.980164,10,0,0.5 +"[M+Cl+HCOOH]-",1,-1,80.974872,11,0,0.5 +"[M+HCOO]-",1,-1,44.99765,12,0,1 +"[M+Cl+CF3COOH]-",1,-1,148.962402,13,0,0.5 +"[M-H+CF3COOH]-",1,-1,112.985724,14,0,0.5 +"[M+Cl+NH3]-",1,-1,51.995952,15,0,0.5 +"[M-H+NH3]-",1,-1,16.019274,16,0,0.5 +"[M-H-CH4]-",1,-1,-17.038576,17,0,0.25 +"[M-H-CO]-",1,-1,-29.002176,18,0,0.25 +"[M-H-C2H2O2]-",1,-1,-47.012746,19,0,0.25 +"[M-H-C3H2O3]-",1,-1,-87.007666,20,0,0.25 +"[M-H-C5H8O4]-",1,-1,-133.049536,21,0,0.25 +"[M-H-C6H10O4]-",1,-1,-147.065186,22,0,0.25 +"[M-H-C6H10O5]-",1,-1,-163.060096,23,0,0.25 +"[M-H-C6H8O6]-",1,-1,-177.039366,24,0,0.25 +"[M-H-H2]-",1,-1,-3.02292607,25,0,0.25 +"[M-H-CH2]-",1,-1,-15.02292607,26,0,0.25 +"[M-H-CH3]-",1,-1,-16.030751105,27,0,0.25 +"[M-H-NH3]-",1,-1,-18.033826,28,0,0.25 +"[M-H-H2O]-",1,-1,-19.0178407,29,0,0.25 +"[M-H-H4O2]-",1,-1,-37.0284054,30,0,0.25 +"[M-H-HF]-",1,-1,-21.013504255,31,0,0.25 +"[M-H-C2H2]-",1,-1,-27.02292607,32,0,0.25 +"[M-H-C2H3]-",1,-1,-28.030751105,33,0,0.25 +"[M-H-HCN]-",1,-1,-28.018175037,34,0,0.25 +"[M-H-C2H4]-",1,-1,-29.03857614,35,0,0.25 +"[M-H-C2H6]-",1,-1,-31.05422621,36,0,0.25 +"[M-H-CH2O]-",1,-1,-31.0178407,37,0,0.25 +"[M-H-CH5N]-",1,-1,-32.049475177,38,0,0.25 +"[M-H-CH4O]-",1,-1,-33.03349077,39,0,0.25 +"[M-H-H2S]-",1,-1,-34.99499677,40,0,0.25 +"[M-H-HCl]-",1,-1,-36.983953755,41,0,0.25 +"[M-H-C3H2]-",1,-1,-39.02292607,42,0,0.25 +"[M-H-C2N]-",1,-1,-39.010350002,43,0,0.25 +"[M-H-F2]-",1,-1,-39.00408244,44,0,0.25 +"[M-H-C3H3]-",1,-1,-40.030751105,45,0,0.25 +"[M-H-HC2N]-",1,-1,-40.018175037,46,0,0.25 +"[M-H-C3H4]-",1,-1,-41.03857614,47,0,0.25 +"[M-H-C3H6]-",1,-1,-43.05422621,48,0,0.25 +"[M-H-C2H2O]-",1,-1,-43.0178407,49,0,0.25 +"[M-H-C3H6]-",1,-1,-43.05422621,50,0,0.25 +"[M-H-NCO]-",1,-1,-43.005264632,51,0,0.25 +"[M-H-CN2H2]-",1,-1,-43.029074074,52,0,0.25 +"[M-H-HCNO]-",1,-1,-44.013089667,53,0,0.25 +"[M-H-C2H4O]-",1,-1,-45.03349077,54,0,0.25 +"[M-H-CO2]-",1,-1,-44.99710526,55,0,0.25 +"[M-H-N2O]-",1,-1,-45.008338634,56,0,0.25 +"[M-H-CONH2]-",1,-1,-45.020914702,57,0,0.25 +"[M-H-NC2H7]-",1,-1,-46.065125247,58,0,0.25 +"[M-H-C2H6O]-",1,-1,-47.04914084,59,0,0.25 +"[M-H-NO2]-",1,-1,-47.000179262,60,0,0.25 +"[M-H-CH4S]-",1,-1,-49.01064684,61,0,0.25 +"[M-H-C4H4]-",1,-1,-53.03857614,62,0,0.25 +"[M-H-C2N2]-",1,-1,-53.013424004,63,0,0.25 +"[M-H-C4H6]-",1,-1,-55.05422621,64,0,0.25 +"[M-H-C4H8]-",1,-1,-57.06987628,65,0,0.25 +"[M-H-C3H6O]-",1,-1,-59.04914084,66,0,0.25 +"[M-H-C4H10]-",1,-1,-59.08552635,67,0,0.25 +"[M-H-C2H5NO]-",1,-1,-60.044389807,68,0,0.25 +"[M-H-C3H8O]-",1,-1,-61.06479091,69,0,0.25 +"[M-H-C2H4O2]-",1,-1,-61.0284054,70,0,0.25 +"[M-H-C2H5Cl]-",1,-1,-65.015253895,71,0,0.25 +"[M-H-C5H4]-",1,-1,-65.03857614,72,0,0.25 +"[M-H-SO2]-",1,-1,-64.96917596,73,0,0.25 +"[M-H-C5H8]-",1,-1,-69.06987628,74,0,0.25 +"[M-H-C5H12]-",1,-1,-73.10117642,75,0,0.25 +"[M-H-C3H6O2]-",1,-1,-75.04405547,76,0,0.25 +"[M-H-C4H10O]-",1,-1,-75.08044098,77,0,0.25 +"[M-H-C6H6]-",1,-1,-79.05422621,78,0,0.25 +"[M-H-CS2]-",1,-1,-76.9514174,79,0,0.25 +"[M-H-C5H5N]-",1,-1,-80.049475177,80,0,0.25 +"[M-H-HBr]-",1,-1,-80.933437135,81,0,0.25 +"[M-H-C2F4]-",1,-1,-101.00088888,82,0,0.25 +"[M-H-C2F6]-",1,-1,-138.99769532,83,0,0.25 +"[M-H-C7H6O2]-",1,-1,-123.04405547,84,0,0.25 +"[M-H-HI]-",1,-1,-128.919574035,85,0,0.25 +"[M-H-H6O3]-",1,-1,-55.0389701,87,0,0.25 +"[M-H-H8O4]-",1,-1,-73.0495348,88,0,0.25 +"[M-H-H10O5]-",1,-1,-91.0600995,89,0,0.25 +"[M-H-H12O6]-",1,-1,-109.0706642,90,0,0.25 +"[M-H-H14O7]-",1,-1,-127.0812289,91,0,0.25 +"[M-H-CH6O3]-",1,-1,-67.0389701,93,0,0.25 +"[M-H-CH4O2]-",1,-1,-49.0284054,94,0,0.25 +"[M-H-NaOH]-",1,-1,-40.999783365,95,0,0.25 +"[M-H-KOH]-",1,-1,-56.973723065,96,0,0.25
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CASMI_extended_POS_rules.csv Fri Apr 07 07:42:18 2017 -0400 @@ -0,0 +1,312 @@ +"name","nmol","charge","massdiff","oidscore","quasi","ips" +"[M+H]+",1,1,1.007276,1,1,1 +"[M+2H]2+",1,2,2.014552,2,0,1 +"[M+3H]3+",1,3,3.021828,3,0,1 +"[M+H+Na]2+",1,2,23.996494,4,0,0.5 +"[M+H+K]2+",1,2,39.970434,6,0,0.5 +"[M+Na]+",1,1,22.989218,7,1,1 +"[M+2Na]2+",1,2,45.978436,8,0,0.75 +"[M+K]+",1,1,38.963158,9,1,1 +"[M+Na+K]2+",1,2,61.952376,10,0,0.75 +"[M+2Na+K]3+",1,3,84.941594,11,0,0.75 +"[M+2K]2+",1,2,77.926316,12,0,0.75 +"[M+Na+2K]3+",1,3,100.915534,13,0,0.75 +"[M+2Na-H]+",1,1,44.97116,15,0,0.25 +"[M+3Na-H]2+",1,2,67.960378,16,0,0.25 +"[M+Na+K-H]+",1,1,60.9451,17,0,0.25 +"[M+2Na+K-H]2+",1,2,83.934318,18,0,0.25 +"[M+3Na+K-H]3+",1,3,106.923536,19,0,0.25 +"[M+Na+2K-H]2+",1,2,99.908258,20,0,0.25 +"[M+2Na+2K-H]3+",1,3,122.897476,21,0,0.25 +"[M+2K-H]+",1,1,76.91904,23,0,0.25 +"[M+3K-H]2+",1,2,115.882198,24,0,0.25 +"[M+Na+3K-H]3+",1,3,138.871416,25,0,0.25 +"[2M+H]+",2,1,1.007276,1,0,0.5 +"[2M+2H]2+",2,2,2.014552,2,0,0.5 +"[2M+3H]3+",2,3,3.021828,3,0,0.5 +"[2M+H+Na]2+",2,2,23.996494,4,0,0.5 +"[2M+H+K]2+",2,2,39.970434,6,0,0.5 +"[2M+Na]+",2,1,22.989218,7,0,0.5 +"[2M+2Na]2+",2,2,45.978436,8,0,0.5 +"[2M+K]+",2,1,38.963158,9,0,0.5 +"[2M+Na+K]2+",2,2,61.952376,10,0,0.5 +"[2M+2Na+K]3+",2,3,84.941594,11,0,0.5 +"[2M+2K]2+",2,2,77.926316,12,0,0.5 +"[2M+Na+2K]3+",2,3,100.915534,13,0,0.5 +"[2M+2Na-H]+",2,1,44.97116,15,0,0.25 +"[2M+3Na-H]2+",2,2,67.960378,16,0,0.25 +"[2M+Na+K-H]+",2,1,60.9451,17,0,0.25 +"[2M+2Na+K-H]2+",2,2,83.934318,18,0,0.25 +"[2M+3Na+K-H]3+",2,3,106.923536,19,0,0.25 +"[2M+Na+2K-H]2+",2,2,99.908258,20,0,0.25 +"[2M+2Na+2K-H]3+",2,3,122.897476,21,0,0.25 +"[2M+2K-H]+",2,1,76.91904,23,0,0.25 +"[2M+3K-H]2+",2,2,115.882198,24,0,0.25 +"[2M+Na+3K-H]3+",2,3,138.871416,25,0,0.25 +"[3M+H]+",3,1,1.007276,1,0,0.5 +"[3M+2H]2+",3,2,2.014552,2,0,0.5 +"[3M+3H]3+",3,3,3.021828,3,0,0.5 +"[3M+H+Na]2+",3,2,23.996494,4,0,0.5 +"[3M+H+K]2+",3,2,39.970434,6,0,0.5 +"[3M+Na]+",3,1,22.989218,7,0,0.5 +"[3M+2Na]2+",3,2,45.978436,8,0,0.5 +"[3M+K]+",3,1,38.963158,9,0,0.5 +"[3M+Na+K]2+",3,2,61.952376,10,0,0.5 +"[3M+2Na+K]3+",3,3,84.941594,11,0,0.5 +"[3M+2K]2+",3,2,77.926316,12,0,0.5 +"[3M+Na+2K]3+",3,3,100.915534,13,0,0.5 +"[3M+2Na-H]+",3,1,44.97116,15,0,0.25 +"[3M+3Na-H]2+",3,2,67.960378,16,0,0.25 +"[3M+Na+K-H]+",3,1,60.9451,17,0,0.25 +"[3M+2Na+K-H]2+",3,2,83.934318,18,0,0.25 +"[3M+3Na+K-H]3+",3,3,106.923536,19,0,0.25 +"[3M+Na+2K-H]2+",3,2,99.908258,20,0,0.25 +"[3M+2Na+2K-H]3+",3,3,122.897476,21,0,0.25 +"[3M+2K-H]+",3,1,76.91904,23,0,0.25 +"[3M+3K-H]2+",3,2,115.882198,24,0,0.25 +"[3M+Na+3K-H]3+",3,3,138.871416,25,0,0.25 +"[M+Na+NaCOOH]+",1,1,90.976658,27,0,0.5 +"[M+K+NaCOOH]+",1,1,106.950598,28,0,0.5 +"[M+Na+HCOOH]+",1,1,68.994688,29,0,0.5 +"[M+K+HCOOH]+",1,1,84.968628,30,0,0.5 +"[M+H+HCOOH]+",1,1,47.012746,31,0,0.5 +"[M+Na+CF3COOH]+",1,1,136.982218,32,0,0.5 +"[M+K+CF3COOH]+",1,1,152.956158,33,0,0.5 +"[M+H+CF3COOH]+",1,1,115.000276,34,0,0.5 +"[M+Na+NH3]+",1,1,40.015768,35,0,0.5 +"[M+K+NH3]+",1,1,55.989708,36,0,0.5 +"[M+H+NH3]+",1,1,18.033826,37,0,0.5 +"[M+H-CH4]+",1,1,-15.024024,38,0,0.25 +"[M+2H-CH4]2+",1,2,-14.016748,39,0,0.25 +"[M+3H-CH4]3+",1,3,-13.009472,40,0,0.25 +"[M+H-CO]+",1,1,-26.987624,41,0,0.25 +"[M+2H-CO]2+",1,2,-25.980348,42,0,0.25 +"[M+3H-CO]3+",1,3,-24.973072,43,0,0.25 +"[M+H-C2H2O2]+",1,1,-44.998194,44,0,0.25 +"[M+2H-C2H2O2]2+",1,2,-43.990918,45,0,0.25 +"[M+3H-C2H2O2]3+",1,3,-42.983642,46,0,0.25 +"[M+H-C3H2O3]+",1,1,-84.993114,47,0,0.25 +"[M+2H-C3H2O3]2+",1,2,-83.985838,48,0,0.25 +"[M+3H-C3H2O3]3+",1,3,-82.978562,49,0,0.25 +"[M+H-C5H8O4]+",1,1,-131.034984,50,0,0.25 +"[M+2H-C5H8O4]2+",1,2,-130.027708,51,0,0.25 +"[M+3H-C5H8O4]3+",1,3,-129.020432,52,0,0.25 +"[M+H-C6H10O4]+",1,1,-145.050634,53,0,0.25 +"[M+2H-C6H10O4]2+",1,2,-144.043358,54,0,0.25 +"[M+3H-C6H10O4]3+",1,3,-143.036082,55,0,0.25 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--- a/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv Wed Feb 01 12:24:04 2017 -0500 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv Fri Apr 07 07:42:18 2017 -0400 @@ -182,7 +182,7 @@ M212T3941 0 0 1197.22500000004 0 M212T3970 155.689673877202 0 838.732800000007 0 M212T3804 0 0 1062.49919999995 0 -M213T3904 0 1230.08999999997 0 0 +M213T3904_1 0 1230.08999999997 0 0 M213T4087 0 0 0 1056.24000000001 M213T3699 0 0 0 2142.48500000007 M213T3793 0 3184.77499999996 0 0 @@ -190,7 +190,7 @@ M213T2688 0 5023.65000000018 0 0 M213T3487 8261.63499999989 0 0 0 M213T4135 1010.12467927487 172.279374858226 0 1228.52499999999 -M213T3904 1081.29983333335 0 700.103750256462 1711.00602968181 +M213T3904_2 1081.29983333335 0 700.103750256462 1711.00602968181 M213T2866 0 9848.54499999999 0 0 M213T3283 0 5371.08000000019 1374.37696617401 1789.50584149986 M213T3836 536.790799509607 0 419.296573102181 5720.0750000002 @@ -335,13 +335,13 @@ M223T3313 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv Fri Apr 07 07:42:18 2017 -0400 @@ -0,0 +1,8158 @@ +name ko15 ko16 wt15 wt16 +M200T2874 76871.5724822568 506848.884266667 54795.557051693 70712.7019597617 +M200T3877 1144.01499999999 508.190132093174 167.153311923928 0 +M200T3676 0 0 5108.15999999988 3298.99587926868 +M200T3486 6029.94499999992 0 0 0 +M200T3529 0 0 4586.52650000006 0 +M200T3184 0 4333.4849999999 0 0 +M200T3817 0 0 1018.81499999998 0 +M200T3978 0 0 0 1242.61000000004 +M201T3544 0 2863.6449999999 0 0 +M201T4063 0 0 1339.64000000005 212.633272048894 +M201T3783 0 0 1680.81000000006 0 +M201T3274 0 1428.56579382624 4090.91000000014 2632.56262635375 +M201T2556 0 14307.2299999999 0 0 +M201T3626 0 1129.74329389996 846.832572052814 2931.24499999993 +M201T3138 23998.304598303 254581.758476187 61872.928839246 23938.5867670927 +M201T3509 4023.61499999999 716.684794188254 0 0 +M201T4066 354.759136757153 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--- a/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Wed Feb 01 12:24:04 2017 -0500 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Fri Apr 07 07:42:18 2017 -0400 @@ -1,8158 +1,8158 @@ -name mz mzmin mzmax rt rtmin rtmax npeaks KO WT isotopes adduct pcgroup fold tstat pvalue -M200T2874 200.100006103516 200.100006103516 200.100006103516 2873.66790279219 2873.66790279219 2873.66790279219 1 1 0 4758 4.65085295060662 -1.06493655910147 0.479605513245819 -M200T3877 200.199996948242 200.199996948242 200.199996948242 3876.72559155354 3876.72559155354 3876.72559155354 1 1 0 2728 9.88436970273782 -2.25887629759232 0.240554009337641 -M200T3676 200.199996948242 200.199996948242 200.199996948242 3676.20857473389 3676.20857473389 3676.20857473389 1 0 1 3702 Inf 4.64698353395969 0.13493854409364 -M200T3486 200.199996948242 200.199996948242 200.199996948242 3485.71318236608 3485.71318236608 3485.71318236608 1 1 0 1771 Inf -1 0.5 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--- a/tool_dependencies.xml Wed Feb 01 12:24:04 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="R" version="3.1.2"> - <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bioconductor-camera" version="1.26.0"> - <repository changeset_revision="fd308c76626b" name="package_bioconductor_camera_1_26_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="graphicsmagick" version="1.3.20"> - <repository changeset_revision="f2855f4cbc8f" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>