Mercurial > repos > lecorguille > camera_annotate
changeset 28:591d26b9027e draft
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
| author | lecorguille |
|---|---|
| date | Tue, 28 Mar 2017 10:51:29 -0400 |
| parents | 04e32b9a5486 |
| children | 59bdfc862408 |
| files | CAMERA.r README.rst abims_CAMERA_annotateDiffreport.xml lib.r macros.xml test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv |
| diffstat | 7 files changed, 16689 insertions(+), 16661 deletions(-) [+] |
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--- a/CAMERA.r Mon Feb 13 11:19:21 2017 -0500 +++ b/CAMERA.r Tue Mar 28 10:51:29 2017 -0400 @@ -98,64 +98,13 @@ #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 -} - -if (!is.null(listArguments[["singlefile_galaxyPath"]])){ - singlefile_galaxyPaths = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL - singlefile_sampleNames = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL - - 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 - } -} - # We unzip automatically the chromatograms from the zip files. if (thefunction %in% c("annotatediff")) { - if(exists("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(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) - } - - #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") - - } + rawFilePath = getRawfilePathFromArguments(listArguments) + zipfile = rawFilePath$zipfile + singlefile = rawFilePath$singlefile + listArguments = rawFilePath$listArguments + directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) }
--- a/README.rst Mon Feb 13 11:19:21 2017 -0500 +++ b/README.rst Tue Mar 28 10:51:29 2017 -0400 @@ -8,10 +8,12 @@ - UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata. -- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants +- IMPROVEMENT: add some sections within the form to separate the different parts of the process - IMPROVEMENT: add the possibility to use defined ruleset +- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants + - IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet @@ -35,12 +37,12 @@ - UPDATE: refactoring of internal management of inputs/outputs -VERSION 2.1.0 - 09/10/2015** +**VERSION 2.1.0 - 09/10/2015** - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) -VERSION 2.1.0 - 07/06/2015** +**VERSION 2.1.0 - 07/06/2015** - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
--- a/abims_CAMERA_annotateDiffreport.xml Mon Feb 13 11:19:21 2017 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Tue Mar 28 10:51:29 2017 -0400 @@ -14,45 +14,62 @@ xfunction annotatediff image '$image' + nSlaves \${GALAXY_SLOTS:-1} + + ## output variableMetadataOutput '$variableMetadata' dataMatrixOutput '$datamatrix' xsetRdataOutput '$rdata' - nSlaves \${GALAXY_SLOTS:-1} - sigma $sigma perfwhm $perfwhm - maxcharge $maxcharge maxiso $maxiso minfrac $minfrac - ppm $ppm mzabs $mzabs - max_peaks $max_peaks + ## groupFWHM + sigma $groupfwhm.sigma + perfwhm $groupfwhm.perfwhm + + ## findIsotopes + maxcharge $findisotopes.maxcharge + maxiso $findisotopes.maxiso + minfrac $findisotopes.minfrac + + ## General + ppm $general.ppm + mzabs $general.mzabs + max_peaks $general.max_peaks + + 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 - #if $quick_block.rules_block.rules_select == "FALSE" - multiplier $quick_block.rules_block.multiplier + ## findadducts + polarity $quick_block.findadducts.polarity + #if $quick_block.findadducts.rules_block.rules_select == "FALSE" + multiplier $quick_block.findadducts.rules_block.multiplier #else - rules $quick_block.rules_block.rules + rules $quick_block.findadducts.rules_block.rules #end if + + ## 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 + #end if + + #if $diffreport.options.option == "show": + ## diffreport + runDiffreport TRUE + 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 + new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ #end if @COMMAND_PEAKLIST@ - #if $options.option == "show": - 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}_ - #end if - @COMMAND_FILE_LOAD@ ]]></command> @@ -62,258 +79,157 @@ <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" /> - <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="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" /> + <section name="groupfwhm" title="Function: 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="findisotopes" title="Function: 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> + + <section name="general" title="General" expanded="True"> + <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="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" /> + </section> <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]"/> - <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> + <section name="findadducts" title="Function: 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> - <when value="FALSE"> - <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"> - <param name="rules" type="data" format="csv" label="findAdducts: User defined ruleset" help="[rules]" /> - </when> - </conditional> + <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> + <section name="groupcorr" title="Function: 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> + </when> <when value="TRUE"> <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" /> </when> </conditional> - <expand macro="input_peaklist"/> + <!-- Diffreport specific parameters --> + <section name="diffreport" title="Function: 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> - <!-- 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="file_load"/> + <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="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" > + <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" > <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> + <filter>(diffreport.options.option == "show")</filter> </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="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="max_peaks" value="100"/> + <expand macro="test_annotate_diffreport"/> <conditional name="quick_block"> - <param name="quick" value="FALSE"/> - <param name="polarity" value="negative"/> - <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"/> - <conditional name="rules_block"> - <param name="rules_select" value="FALSE"/> - <param name="multiplier" value="3"/> - </conditional> + <expand macro="test_annotate_diffreport_quick" /> + <section name="findadducts"> + <param name="polarity" value="negative"/> + <conditional name="rules_block"> + <param name="rules_select" value="FALSE"/> + <param name="multiplier" value="3"/> + </conditional> + </section> </conditional> - <param name="convertRTMinute" value="False"/> - <param name="numDigitsMZ" value="4" /> - <param name="numDigitsRT" value="1" /> - <param name="intval" value="into"/> - <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> - <param name="file_load_conditional|file_load_select" value="yes" /> - <param name="file_load_conditional|inputs|input" value="zip_file" /> - <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <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"/> - <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="max_peaks" value="100"/> + <expand macro="test_annotate_diffreport"/> <conditional name="quick_block"> - <param name="quick" value="FALSE"/> - <param name="polarity" value="negative"/> - <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"/> - <conditional name="rules_block"> - <param name="rules_select" value="FALSE"/> - <param name="multiplier" value="3"/> - </conditional> + <expand macro="test_annotate_diffreport_quick" /> + <section name="findadducts"> + <param name="polarity" value="negative"/> + <conditional name="rules_block"> + <param name="rules_select" value="FALSE"/> + <param name="multiplier" value="3"/> + </conditional> + </section> </conditional> - <param name="convertRTMinute" value="False"/> - <param name="numDigitsMZ" value="4" /> - <param name="numDigitsRT" value="1" /> - <param name="intval" value="into"/> - <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> - <param name="file_load_conditional|file_load_select" value="yes" /> - <param name="file_load_conditional|inputs|input" value="single_file" /> - <param name="file_load_conditional|inputs|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + <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"/> - <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="max_peaks" value="100"/> + <expand macro="test_annotate_diffreport"/> <conditional name="quick_block"> - <param name="quick" value="FALSE"/> - <param name="polarity" value="negative"/> - <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"/> - <conditional name="rules_block"> - <param name="rules_select" value="TRUE"/> - <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/> - </conditional> + <expand macro="test_annotate_diffreport_quick" /> + <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> - <param name="convertRTMinute" value="False"/> - <param name="numDigitsMZ" value="4" /> - <param name="numDigitsRT" value="1" /> - <param name="intval" value="into"/> - <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> - <param name="file_load_conditional|file_load_select" value="yes" /> - <param name="file_load_conditional|inputs|input" value="single_file" /> - <param name="file_load_conditional|inputs|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + <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> @@ -370,7 +286,7 @@ +---------------------------+---------------------------------------+------------------------------------------------+ | 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 | +---------------------------+---------------------------------------+------------------------------------------------+ @@ -408,6 +324,22 @@ +---------------------------+---------------------------+ +[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 ---------- @@ -501,16 +433,18 @@ Changelog/News -------------- -**Version 2.2.0 - 03/02/2017** +**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 the possibility to set the MZ digit within the identifiants +- 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 @@ -535,12 +469,12 @@ - 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.
--- a/lib.r Mon Feb 13 11:19:21 2017 -0500 +++ b/lib.r Tue Mar 28 10:51:29 2017 -0400 @@ -223,3 +223,84 @@ return(variableMetadata); } + +# This function get the raw file path from the arguments +getRawfilePathFromArguments <- function(listArguments) { + zipfile = NULL + singlefile = NULL + 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 Mon Feb 13 11:19:21 2017 -0500 +++ b/macros.xml Tue Mar 28 10:51:29 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"> @@ -20,61 +19,124 @@ LANG=C Rscript $__tool_directory__/CAMERA.r </token> - <!-- zipfile load for planemo test --> + <!-- raw file load for planemo test --> <token name="@COMMAND_FILE_LOAD@"> - #if $file_load_conditional.file_load_select == "yes": - #if $file_load_conditional.inputs.input == "zip_file": - zipfile '$file_load_conditional.inputs.zip_file' + #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 - #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] ) - #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] ) - - singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + zipfile '$file_load_section.file_load_conditional.input' #end if #end if </token> - <xml name="file_load"> - <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"> - <conditional name="inputs"> - <param name="input" type="select" label="Choose your inputs method" > - <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> - <option value="single_file">A mzXML or netCDF file from your history</option> - </param> - <when value="zip_file"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - <when value="single_file"> - <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/> - </when> - </conditional> - </when> - </conditional> + <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 $convertRTMinute - numDigitsMZ $numDigitsMZ - numDigitsRT $numDigitsRT - intval $intval + convertRTMinute $export.convertRTMinute + numDigitsMZ $export.numDigitsMZ + numDigitsRT $export.numDigitsRT + intval $export.intval </token> <xml name="input_peaklist"> - <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 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="general"> + <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_diffreport_quick"> + <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> <token name="@HELP_AUTHORS@">
--- a/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv Mon Feb 13 11:19:21 2017 -0500 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv Tue Mar 28 10:51:29 2017 -0400 @@ -1,8158 +1,8158 @@ name namecustom mz mzmin mzmax rt rtmin rtmax npeaks KO WT isotopes adduct pcgroup fold tstat pvalue -M200T2874 M200.1T2873.7 200.100006103516 200.100006103516 200.100006103516 2873.66790279219 2873.66790279219 2873.66790279219 1 1 0 4758 4.65085295060662 -1.06493655910147 0.479605513245819 -M200T3877 M200.2T3876.7 200.199996948242 200.199996948242 200.199996948242 3876.72559155354 3876.72559155354 3876.72559155354 1 1 0 2728 9.88436970273782 -2.25887629759232 0.240554009337641 -M200T3676 M200.2T3676.2 200.199996948242 200.199996948242 200.199996948242 3676.20857473389 3676.20857473389 3676.20857473389 1 0 1 3702 Inf 4.64698353395969 0.13493854409364 -M200T3486 M200.2T3485.7 200.199996948242 200.199996948242 200.199996948242 3485.71318236608 3485.71318236608 3485.71318236608 1 1 0 1771 Inf -1 0.5 -M200T3529 M200.2T3529.2 200.199996948242 200.199996948242 200.199996948242 3529.16673849327 3529.16673849327 3529.16673849327 1 0 1 370 Inf 1 0.5 -M200T3184 M200.2T3184.4 200.199996948242 200.199996948242 200.199996948242 3184.44736675265 3184.44736675265 3184.44736675265 1 1 0 40 Inf -1 0.5 -M200T3817 M200.3T3816.6 200.300003051758 200.300003051758 200.300003051758 3816.57302395962 3816.57302395962 3816.57302395962 1 0 1 2375 Inf 1 0.5 -M200T3978 M200.3T3977.6 200.300003051758 200.300003051758 200.300003051758 3977.60008277685 3977.60008277685 3977.60008277685 1 0 1 1981 Inf 1 0.5 -M201T3544 M200.8T3543.6 200.800003051758 200.800003051758 200.800003051758 3543.60312635477 3543.60312635477 3543.60312635477 1 1 0 2331 Inf -1 0.5 -M201T4063 M200.8T4062.6 200.800003051758 200.800003051758 200.800003051758 4062.56884383761 4062.56884383761 4062.56884383761 1 0 1 213 Inf 1.37734161966442 0.399789013602801 -M201T3783 M200.8T3783.3 200.800003051758 200.800003051758 200.800003051758 3783.31394298599 3783.31394298599 3783.31394298599 1 0 1 3662 Inf 1 0.5 -M201T3274 M200.9T3273.9 200.900009155273 200.900009155273 200.900009155273 3273.93376916172 3273.93376916172 3273.93376916172 1 0 1 5027 4.70644940219791 2.59368058676224 0.122082365514126 -M201T2556 M200.9T2555.9 200.900009155273 200.900009155273 200.900009155273 2555.90497459635 2555.90497459635 2555.90497459635 1 1 0 3065 Inf -1 0.5 -M201T3626 M200.9T3625.9 200.900009155273 200.900009155273 200.900009155273 3625.94998801881 3625.94998801881 3625.94998801881 1 0 1 1600 3.34419119144363 1.11702356726728 0.408252476299869 -M201T3138 M201.1T3138.4 201.100006103516 201.100006103516 201.100006103516 3138.35441665664 3138.35441665664 3138.35441665664 1 1 0 67 3.24641816551149 -0.824914731473309 0.555087522533288 -M201T3509 M201.2T3509.4 201.199996948242 201.199996948242 201.199996948242 3509.36563736658 3509.36563736658 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--- a/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Mon Feb 13 11:19:21 2017 -0500 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Tue Mar 28 10:51:29 2017 -0400 @@ -1,8158 +1,8158 @@ name namecustom mz mzmin mzmax rt rtmin rtmax npeaks KO WT isotopes adduct pcgroup fold tstat pvalue -M200T2874 M200.1T2873.7 200.100006103516 200.100006103516 200.100006103516 2873.66790279219 2873.66790279219 2873.66790279219 1 1 0 4758 4.65085295060662 -1.06493655910147 0.479605513245819 -M200T3877 M200.2T3876.7 200.199996948242 200.199996948242 200.199996948242 3876.72559155354 3876.72559155354 3876.72559155354 1 1 0 2728 9.88436970273782 -2.25887629759232 0.240554009337641 -M200T3676 M200.2T3676.2 200.199996948242 200.199996948242 200.199996948242 3676.20857473389 3676.20857473389 3676.20857473389 1 0 1 3702 Inf 4.64698353395969 0.13493854409364 -M200T3486 M200.2T3485.7 200.199996948242 200.199996948242 200.199996948242 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568.400024414062 568.400024414062 568.400024414062 3788.06929478123 3788.06929478123 3788.06929478123 1 0 1 4445 2.13216621360993 0.510855550855557 0.685358887271267 -M568T3691 M568.4T3690.7 568.400024414062 568.400024414062 568.400024414062 3690.69884839 3690.69884839 3690.69884839 1 1 0 [148][M+1]- 5 15.5543130492561 -0.994766360860313 0.501594252160052 -M568T3688 M568.5T3687.7 568.5 568.5 568.5 3687.71946612331 3687.71946612331 3687.71946612331 1 0 1 616 Inf 1 0.5 -M568T3157 M568.5T3156.7 568.5 568.5 568.5 3156.6778024024 3156.6778024024 3156.6778024024 1 1 0 820 Inf -1 0.5 -M568T2567 M568.5T2567.2 568.5 568.5 568.5 2567.15228676082 2567.15228676082 2567.15228676082 1 1 0 5868 7.24095262006366 -0.853793078290496 0.545832132859072 -M569T2621 M568.8T2621 568.799987792969 568.799987792969 568.799987792969 2620.96079482671 2618.50297459635 2623.41861505708 2 1 1 2687 2.05196461220416 0.622732899861801 0.601912715122086 -M569T3448 M568.8T3448.1 568.799987792969 568.799987792969 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569.400024414062 569.400024414062 569.400024414062 3793.87289826827 3789.65430237007 3798.09149416646 2 1 1 5407 1.10849904514587 0.0757587381299332 0.946510971961744 -M569T3760 M569.4T3759.7 569.400024414062 569.400024414062 569.400024414062 3759.66571973942 3759.66571973942 3759.66571973942 1 0 1 935 7.3089146587618 2.4802310086677 0.240387379588944 -M569T3691 M569.4T3690.9 569.400024414062 569.400024414062 569.400024414062 3690.87159551378 3690.87159551378 3690.87159551378 1 1 0 [148][M+2]- 627 3.93642452049446 -2.5328967072787 0.158790771552546 -M569T2747 M569.4T2746.5 569.400024414062 569.400024414062 569.400024414062 2746.52752074663 2746.52752074663 2746.52752074663 1 0 1 4364 4.20166680243049 0.741293344704183 0.583409105199133 -M570T2712 M569.5T2711.6 569.5 569.5 569.5 2711.57727406938 2711.57727406938 2711.57727406938 1 1 0 2532 Inf -1 0.5 -M570T2898 M569.5T2897.9 569.5 569.5 569.5 2897.94212950607 2897.94212950607 2897.94212950607 1 1 0 4783 Inf -1 0.5 -M570T3941 M569.5T3941.2 569.5 569.5 569.5 3941.16625793116 3941.16625793116 3941.16625793116 1 0 1 4172 3.56876855030395 1.21719671534725 0.378123805670911 -M570T3637 M569.5T3637.4 569.5 569.5 569.5 3637.35902306758 3637.35902306758 3637.35902306758 1 0 1 2857 Inf 1 0.5 -M570T4103 M569.5T4103.2 569.5 569.5 569.5 4103.18433006527 4103.18433006527 4103.18433006527 1 1 0 6178 Inf -1 0.5 -M570T4078 M569.5T4078.3 569.5 569.5 569.5 4078.279061465 4078.279061465 4078.279061465 1 1 0 3910 Inf -1 0.5 -M570T2893 M569.6T2892.6 569.600036621094 569.600036621094 569.600036621094 2892.58722465327 2892.58722465327 2892.58722465327 1 1 0 95 Inf -1 0.5 -M570T2761 M569.7T2761.4 569.700012207031 569.700012207031 569.700012207031 2761.41308680454 2761.41308680454 2761.41308680454 1 0 1 3814 Inf 1 0.5 -M570T2739 M569.8T2739.2 569.799987792969 569.799987792969 569.799987792969 2739.23289356565 2739.23289356565 2739.23289356565 1 0 1 4441 2.46890724640897 0.551445731713441 0.660070214966537 -M570T2919 M569.8T2919 569.799987792969 569.799987792969 569.799987792969 2919.04838573748 2919.04838573748 2919.04838573748 1 1 0 56 1024.94599566422 -1.00208548567273 0.499336606950729 -M570T2611 M569.8T2611 569.799987792969 569.799987792969 569.799987792969 2610.97128676082 2610.97128676082 2610.97128676082 1 1 0 100 4.38434163701072 -0.752588009683133 0.57943768125129 -M570T3287 M570T3286.5 570 570 570 3286.54221079343 3286.54221079343 3286.54221079343 1 0 1 3797 Inf 1 0.5 -M570T3052 M570.1T3051.8 570.100036621094 570.100036621094 570.100036621094 3051.82258433502 3047.63518465713 3056.0099840129 2 1 1 [152][M]- [M-2H+Na]- 549.112 [M-H]- 571.112 81 1.49247950488862 0.282215414858782 0.808042653715397 -M570T3104 M570.1T3103.7 570.100036621094 570.100036621094 570.100036621094 3103.74459948594 3099.07166399095 3108.41753498094 2 1 1 [153][M]- [M-H]- 571.112 68 1.64246000102652 0.409542058107211 0.732461743299891 -M570T3650 M570.1T3649.8 570.100036621094 570.100036621094 570.100036621094 3649.75436085664 3649.75436085664 3649.75436085664 1 1 0 1526 11.8661720305616 -1.88417513925803 0.2993272891737 -M570T3519 M570.1T3518.8 570.100036621094 570.100036621094 570.100036621094 3518.81181544796 3518.81181544796 3518.81181544796 1 1 0 429 Inf -1 0.5 -M570T2542 M570.1T2541.8 570.100036621094 570.100036621094 570.100036621094 2541.81997459635 2541.81997459635 2541.81997459635 1 1 0 5556 2.08937010775257 -0.564233147581743 0.639829357463063 -M570T3132 M570.2T3132.1 570.200012207031 570.200012207031 570.200012207031 3132.1092416445 3132.1092416445 3132.1092416445 1 0 1 5003 Inf 1.58687867835816 0.35797570823539 -M570T3498 M570.3T3498 570.299987792969 570.299987792969 570.299987792969 3497.95028595429 3495.99683372091 3499.90373818767 2 1 1 [M-2H+Na]- 549.312 76 2.52571477419942 -0.59927315985362 0.65376421220146 -M570T4122 M570.3T4122.1 570.299987792969 570.299987792969 570.299987792969 4122.12184262002 4122.06642147928 4122.17726376076 2 2 0 [154][M]- 29 3.2628883784924 -2.06119484688728 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570.600036621094 2727.91346287142 2727.91346287142 2727.91346287142 1 1 0 2448 Inf -1 0.5 -M571T2903 M570.6T2903.2 570.600036621094 570.600036621094 570.600036621094 2903.17727640216 2903.17727640216 2903.17727640216 1 0 1 3926 Inf 1 0.5 -M571T3515 M570.6T3515 570.600036621094 570.600036621094 570.600036621094 3514.99046491624 3514.99046491624 3514.99046491624 1 1 0 [156][M]2- 351 7.98020123951961 -0.905807077098373 0.527375786602802 -M571T2916 M570.8T2916 570.799987792969 570.799987792969 570.799987792969 2915.96882550519 2915.96882550519 2915.96882550519 1 1 0 56 12.3309088179579 -0.916505850244478 0.526440295862228 -M571T2687 M570.8T2687.3 570.799987792969 570.799987792969 570.799987792969 2687.30875175009 2687.30875175009 2687.30875175009 1 0 1 678 2.54636764914849 0.565257337131289 0.653767536308415 -M571T3494 M570.9T3493.6 570.900024414062 570.900024414062 570.900024414062 3493.60089329966 3493.60089329966 3493.60089329966 1 1 0 3512 Inf -11.3238705764385 0.0560738114063082 -M571T3479 M570.9T3479.2 570.900024414062 570.900024414062 570.900024414062 3479.15909272518 3479.15909272518 3479.15909272518 1 0 1 1813 Inf 1 0.5 -M571T3549 M570.9T3548.8 570.900024414062 570.900024414062 570.900024414062 3548.83214501254 3548.83214501254 3548.83214501254 1 1 0 2330 Inf -1 0.5 -M571T3503 M571T3503.1 571 571 571 3503.10417845746 3500.58472682777 3505.62363008716 2 1 1 [M+Cl]- 536.034 [M-2H+Na]- 550.029 [M-H-CH2]- 586.011 76 7.66350778580378 -0.865527859209963 0.543686556622211 -M571T2909 M571T2909.4 571 571 571 2909.41319283123 2909.41319283123 2909.41319283123 1 0 1 56 2.62693531249341 0.610041996475191 0.646455628610895 -M571T2617 M571T2617.1 571 571 571 2617.084668269 2617.084668269 2617.084668269 1 0 1 5640 1.24929180264475 0.579593721956761 0.665596141354144 -M571T3231 M571T3230.5 571 571 571 3230.50925543061 3230.50925543061 3230.50925543061 1 0 1 2726 Inf 1 0.5 -M571T3391 M571T3391.3 571 571 571 3391.28651330641 3391.28651330641 3391.28651330641 1 0 1 499 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