Mercurial > repos > lecorguille > ipo
changeset 1:ae8de756dfcf draft
"planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
| author | workflow4metabolomics |
|---|---|
| date | Mon, 16 Dec 2019 05:26:42 -0500 |
| parents | ac5f2936575b |
| children | 8e5f667359cb |
| files | README.rst ipo4retgroup.r ipo4retgroup.xml ipo4xcmsSet.r ipo4xcmsSet.xml lib.r macros.xml planemo_test.sh repository_dependencies.xml test-data/MM-xset-merge.RData test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv test-data/MM8.mzML test-data/MM_IPO_parameters4retgroup.tsv test-data/faahKO.xset.RData test-data/faahKO.xset.RData2 test-data/faahKO.xset_single.RData test-data/faahKO_IPO_parameters4retgroup_bw.tsv test-data/faahKO_reduce.zip test-data/ko15.CDF test-data/ko16.CDF test-data/sacuri_2files.zip test-data/sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv test-data/sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv test-data/wt15.CDF test-data/wt16.CDF |
| diffstat | 25 files changed, 389 insertions(+), 6984 deletions(-) [+] |
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--- a/README.rst Thu Aug 03 06:00:00 2017 -0400 +++ b/README.rst Mon Dec 16 05:26:42 2019 -0500 @@ -2,13 +2,7 @@ Changelog/News -------------- -**Version X.X.X - XX/XX/XXXX** - -- NEW: +**Version 1.10.0.0 - 03/09/2019** -Test Status ------------ +- NEW: new versions of the IPO wrappers based on IPO-1.10.0 -Planemo test using conda: failed on the faahKO_reduce.zip - -Planemo shed_test : unbuild
--- a/ipo4retgroup.r Thu Aug 03 06:00:00 2017 -0400 +++ b/ipo4retgroup.r Mon Dec 16 05:26:42 2019 -0500 @@ -2,155 +2,66 @@ #Authors Gildas Le Corguille and Yann Guitton -# ----- LOG FILE ----- -log_file=file("log.txt", open = "wt") -sink(log_file) -sink(log_file, type = "output") - +# ----- PACKAGE ----- +cat("\tSESSION INFO\n") -# ----- PACKAGE ----- -options(bitmapType='cairo') -cat("\tPACKAGE INFO\n") -#pkgs=c("xcms","batch") -pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch") -for(pkg in pkgs) { - suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) - cat(pkg,"\t",as.character(packageVersion(pkg)),"\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="/")) } +#Import the different functions +source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +source_local("lib.r") + +pkgs <- c("IPO","batch") +loadAndDisplayPackages(pkgs) cat("\n\n"); # ----- ARGUMENTS ----- cat("\tARGUMENTS INFO\n") -listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects -write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') +args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(args), col.names=F, quote=F, sep='\t') cat("\n\n"); -# ----- ARGUMENTS PROCESSING ----- -cat("\tINFILE PROCESSING INFO\n") - -#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 -} - -#Import the different functions -source_local("lib.r") - -cat("\n\n") - -#Import the different functions - # ----- PROCESSING INFILE ----- cat("\tARGUMENTS PROCESSING INFO\n") - -parametersOutput = "parametersOutput.tsv" -if (!is.null(listArguments[["parametersOutput"]])){ - parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL -} - samplebyclass = 2 -if (!is.null(listArguments[["samplebyclass"]])){ - samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL -} - -#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_galaxyPath = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL - singlefile_sampleName = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL +if (!is.null(args$samplebyclass)){ + samplebyclass = args$samplebyclass; args$samplebyclass=NULL } -# single file case -#@TODO: need to be refactoring -if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) { - - cwd=getwd() - dir.create("raw") - setwd("raw") - - for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPath))) { - if(!file.exists(singlefile_galaxyPath[singlefile_galaxyPath_i])){ - error_message=paste("Cannot access the sample:",singlefile_sampleName[singlefile_galaxyPath_i],"located:",singlefile_galaxyPath[singlefile_galaxyPath_i],". Please, contact your administrator ... if you have one!") - print(error_message); stop(error_message) - } - file.symlink(singlefile_galaxyPath[singlefile_galaxyPath_i],singlefile_sampleName[singlefile_galaxyPath_i]) - } - - setwd(cwd) - - directory = "raw" - -} - -# We unzip automatically the chromatograms from the zip files. -if(exists("zipfile") && (zipfile!="")) { - if(!file.exists(zipfile)){ - error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") - print(error_message) - stop(error_message) - } - - #list all file in the zip file - #zip_files=unzip(zipfile,list=T)[,"Name"] - - # Because IPO only want raw data in its working directory - dir.create("ipoworkingdir") - setwd("ipoworkingdir") - - #unzip - suppressWarnings(unzip(zipfile, unzip="unzip")) - - #get the directory name - filesInZip=unzip(zipfile, list=T); - directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); - directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] - directory = "." - if (length(directories) == 1) directory = directories - - cat("files_root_directory\t",directory,"\n") - - -} - -#addition of the directory to the list of arguments in the first position -checkXmlStructure(directory) -checkFilesCompatibilityWithXcms(directory) - cat("\n\n") +# ----- INFILE PROCESSING ----- +cat("\tINFILE PROCESSING INFO\n") +options(bitmapType='cairo') + +#image is an .RData file necessary to use xset variable given by previous tools +load(args$image); args$image=NULL + +# Because so far CAMERA isn't compatible with the new XCMSnExp object +if (exists("xdata")){ + xset <- getxcmsSetObject(xdata) +} + +if (!exists("xset")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata' which is provided by the tool: MSnbase readMSData") +# Handle infiles +if (!exists("singlefile")) singlefile <- NULL +rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args) +singlefile <- rawFilePath$singlefile +print(singlefile) +directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL) +cat("\n\n") + # ----- MAIN PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") - -ipo4retgroup(xset, directory, parametersOutput, listArguments, samplebyclass) - - - -cat("\n\n") - - -# ----- EXPORT ----- - -cat("\tEXPORTING INFO\n") - -#save.image(file="ipo-retcor.RData") +ipo4retgroup(xset, directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass) cat("\n\n")
--- a/ipo4retgroup.xml Thu Aug 03 06:00:00 2017 -0400 +++ b/ipo4retgroup.xml Mon Dec 16 05:26:42 2019 -0500 @@ -1,24 +1,15 @@ -<tool id="ipo4retgroup" name="IPO for group and retcor" version="0.0.1"> +<tool id="ipo4retgroup" name="IPO for group and retcor" version="@TOOL_VERSION@+galaxy0"> - <description>IPO optimization process for xcms.group and xcms.retcor</description> + <description>IPO optimization process for xcms.groupChromPeaks and xcms.adjustRtime</description> <macros> <import>macros.xml</import> - - <macro name="group_density_bw_fixed"> - <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" /> - </macro> - - <macro name="group_density_mzwid_fixed"> - <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " /> - </macro> </macros> <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ - LANG=C Rscript $__tool_directory__/ipo4retgroup.r + <command detect_errors="exit_code"><![CDATA[ + LANG=C Rscript '$__tool_directory__/ipo4retgroup.r' image '$image' @@ -31,19 +22,19 @@ ## group methods sleep 0.001 - #if $group.methods.method == "density": - bw "c($group.methods.section_group_density_optiomizable.conditional_parameter.bw)" - mzwid "c($group.methods.section_group_density_optiomizable.conditional_parameter.mzwid)" + #if $group.method == "density": + bw "c($group.section_group_density_optiomizable.bw)" + mzwid "c($group.section_group_density_optiomizable.mzwid)" - minfrac $group.methods.section_group_density_non_optimizable.minfrac - max $group.methods.section_group_density_non_optimizable.max + minfrac $group.section_group_density_non_optimizable.minfrac + max $group.section_group_density_non_optimizable.max #end if ## retcor methods #if $retcor.methods.method == "obiwarp": retcorMethod obiwarp - profStep $methods.section_retcor_obiwarp_non_optimizable.profStep + profStep $retcor.methods.section_retcor_obiwarp_non_optimizable.profStep #elif $retcor.methods.method == "peakgroups": retcorMethod loess @@ -58,74 +49,58 @@ #end if @COMMAND_FILE_LOAD@ - - @COMMAND_LOG_EXIT@ ]]></command> <inputs> <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> - <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" /> + <param name="samplebyclass" type="integer" value="2" min="0" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" /> - <section name="group" title="Group Options" expanded="True"> - <conditional name="methods"> - <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below. Only the density method is available so far"> - <option value="density" selected="true">density</option> + <section name="group" title="groupChromPeaks Options" expanded="True"> + <param argument="method" type="select" label="Method to use for grouping" help="See the help section below. Only the density method is available so far"> + <option value="density" selected="true">density</option> + </param> + <section name="section_group_density_optiomizable" title="Optimizable parameters" expanded="True"> + <param argument="bw" type="text" value="22,38" label="Range or a fixed value for Bandwidth" help="bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 22,38)"> + <expand macro="input_validator_range_integer"/> </param> - <when value="density"> - <section name="section_group_density_optiomizable" title="Optimizable parameters" expanded="True"> - <conditional name="conditional_parameter"> - <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> - <option value="bw">Bandwidth [bw]</option> - <option value="mzwid">Width of overlapping m/z slices [mzwid]</option> - </param> - <when value="bw"> - <param name="bw" type="text" value="22,38" label="Range for Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 22,38)"> - <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator> - </param> - <expand macro="group_density_mzwid_fixed" /> - </when> - <when value="mzwid"> - <param name="mzwid" type="text" value="0.015,0.035" label="Range for Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.015,0.035)" > - <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> - </param> - <expand macro="group_density_bw_fixed" /> - </when> - </conditional> - </section> - <section name="section_group_density_non_optimizable" title="Non optimizable parameters" expanded="True"> - <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" /> - <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" /> - </section> - </when> - </conditional> + <param argument="mzwid" type="text" value="0.015,0.035" label="Range or a fixed value for Width of overlapping m/z slices" help="to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.015,0.035)" > + <expand macro="input_validator_range_float_neg"/> + </param> + </section> + <section name="section_group_density_non_optimizable" title="Non optimizable parameters" expanded="True"> + <param argument="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="in at least one of the sample groups for it to be a valid group" /> + <param argument="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" /> + </section> </section> - <section name="retcor" title="Retcor Options" expanded="True"> + <section name="retcor" title="adjustRtime Options" expanded="True"> <conditional name="methods"> - <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > + <param argument="method" type="select" label="Method to use for retention time correction" help="See the help section below" > <option value="obiwarp">obiwarp</option> <option value="peakgroups">peakgroups</option> </param> <when value="obiwarp"> <section name="section_retcor_obiwarp_non_optimizable" title="Non optimizable parameters" expanded="True"> - <param name="profStep" type="text" value="0.7,1.0" label="Range for Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" /> + <param argument="profStep" type="text" value="0.7,1.0" label="Range or a fixed value for Step size (in m/z)" help="to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" > + <expand macro="input_validator_range_float_neg"/> + </param> </section> </when> <when value="peakgroups"> <section name="section_retcor_peakgroups_non_optimizable" title="Non optimizable parameters" expanded="True"> - <param name="smooth" type="select" label="Smooth method" help="[smooth] only the 'loess’ for non-linear alignment is available so far" > + <param argument="smooth" type="select" label="Smooth method" help="only the 'loess’ for non-linear alignment is available so far" > <option value="loess">loess</option> </param> - <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" /> - <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" /> - <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> - <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> + <param argument="extra" type="integer" value="1" min="0" label="Number of extra peaks to allow in retention time correction correction groups" /> + <param argument="missing" type="integer" value="1" min="0" label="Number of missing samples to allow in retention time correction groups" /> + <param argument="span" type="float" value="0.2" min="0" label="Degree of smoothing for local polynomial regression fitting" /> + <param argument="family" type="select" label="Family" help="if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> <option value="gaussian" selected="true">gaussian</option> <option value="symmetric">symmetric</option> </param> - <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> + <param argument="plottype" type="select" help="if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> <option value="none" selected="true">none</option> <option value="deviation">deviation</option> <option value="mdevden">mdevden</option> @@ -141,41 +116,22 @@ </inputs> <outputs> - <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" /> - <data name="log" format="txt" label="ipo4xcmsSet.log.txt" /> + <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" from_work_dir="IPO_parameters4xcmsSet.tsv"/> </outputs> <tests> - <!-- TOO LONG <test> - <param name="image" value="faahKO.xset.RData"/> - <param name="group|methods|method" value="density"/> - <param name="group|methods|bw" value="28,32"/> - <param name="group|methods|minfrac" value="1"/> - <param name="group|methods|mzwid" value="0.15,0.35"/> - <param name="retcor|methods|method" value="peakgroups"/> - <param name="retcor|methods|smooth" value="loess"/> - <param name="retcor|methods|extra" value="1"/> - <param name="retcor|methods|missing" value="1"/> - <expand macro="test_file_load_zip"/> - <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" /> - </test>--> - - <test> - <param name="image" value="faahKO.xset.RData"/> + <param name="image" value="faahKO.xset_single.RData"/> + <param name="samplebyclass" value="0"/> <section name="group"> - <conditional name="methods"> - <param name="method" value="density"/> - <section name="section_group_density_optiomizable"> - <conditional name="conditional_parameter"> - <param name="bw" value="28,32"/> - <param name="mzwid" value="0.25"/> - </conditional> - </section> - <section name="section_group_density_non_optimizable"> - <param name="minfrac" value="1"/> - </section> - </conditional> + <param name="method" value="density"/> + <section name="section_group_density_optiomizable"> + <param name="bw" value="5,6"/> + <param name="mzwid" value="0.01,0.02"/> + </section> + <section name="section_group_density_non_optimizable"> + <param name="minfrac" value="1"/> + </section> </section> <section name="retcor"> <conditional name="methods"> @@ -187,38 +143,9 @@ </section> </conditional> </section> - <expand macro="test_file_load_zip"/> + <expand macro="test_file_load_single"/> <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_bw.tsv" /> </test> - - <!--<test> - <param name="image" value="faahKO.xset.RData"/> - <param name="group|methods|method" value="density"/> - <param name="group|methods|bw" value="30"/> - <param name="group|methods|minfrac" value="1"/> - <param name="group|methods|mzwid" value="0.15,0.35"/> - <param name="retcor|methods|method" value="peakgroups"/> - <param name="retcor|methods|smooth" value="loess"/> - <param name="retcor|methods|extra" value="1"/> - <param name="retcor|methods|missing" value="1"/> - <expand macro="test_file_load_zip"/> - <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_mzmid.tsv" /> - </test>--> - - <!--<test> - <param name="image" value="MM-xset-merge.RData"/> - <param name="group|methods|method" value="density"/> - <param name="group|methods|bw" value="22,38"/> - <param name="group|methods|minfrac" value="1"/> - <param name="group|methods|mzwid" value="0.015,0.035"/> - <param name="retcor|methods|method" value="peakgroups"/> - <param name="retcor|methods|smooth" value="loess"/> - <param name="retcor|methods|extra" value="1"/> - <param name="retcor|methods|missing" value="1"/> - <param name="file_load_conditional|file_load_select" value="yes" /> - <expand macro="test_file_load_single"/> - <output name="parametersOutput" file="MM_IPO_parameters4retgroup.tsv" /> - </test>--> </tests> <help><![CDATA[ @@ -242,11 +169,13 @@ **Upstream tools** -========================= ================= ======= ========= -Name output file format parameter -========================= ================= ======= ========= -NA NA zip NA -========================= ================= ======= ========= +==================================== ======================== ============================== +Name Output file Format +==================================== ======================== ============================== +xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks +------------------------------------ ------------------------ ------------------------------ +xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor +==================================== ======================== ============================== **Downstream tools** @@ -254,109 +183,48 @@ +---------------------------+----------------------+-----------------+ | Name | Output file | Format | +===========================+======================+=================+ -|xcms.xcmsSet | parametersOutput.tsv | Tabular | +|xcms.groupChromPeaks | parametersOutput.tsv | Tabular | +---------------------------+--------------------+-------------------+ - ------------ -Input files ------------ - -+---------------------------+------------+ -| Parameter : num + label | Format | -+===========================+============+ -| 1 : Choose your inputs | zip | -+---------------------------+------------+ - -**Choose your inputs** - -You have two methods for your inputs: - - | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). - | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories. - -Steps for creating the zip file -------------------------------- - -**Step1: Creating your directory and hierarchize the subdirectories** - - -VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug). - -Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild): -arabidopsis/wild/01.raw -arabidopsis/mutant/01.raw - -**Step2: Creating a zip file** - -Create your zip file (e.g.: arabidopsis.zip). - -**Step 3 : Uploading it to our Galaxy server** - -If your zip file is less than 2Gb, you get use the Get Data tool to upload it. - -Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf). - -For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org). - -Advices for converting your files for the XCMS input ----------------------------------------------------- - -We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method. - -**We recommend you the following parameters:** - -Use Filtering: **True** - -Use Peak Picking: **True** - -Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode - -Use zlib: **64** - -Binary Encoding: **64** - -m/z Encoding: **64** - -Intensity Encoding: **64** - - ---------- Parameters ---------- -Extraction method for peaks detection -------------------------------------- +Method to use for groupChromPeaks +--------------------------------- + +**PeakDensity** -**Matched Filter** + | This method performs performs correspondence (chromatographic peak grouping) based on the density (distribution) of identified peaks along the retention time axis within slices of overlapping mz ranges. All peaks (from the same or from different samples) being close on the retention time axis are grouped into a feature (peak group). + | See the PeakDensity_manual_ - | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. - | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002). + +.. _PeakDensity_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-density.html#heading-2 -**cent Wave** +Method to use for adjustRtime +------------------------------------------- - | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode. - | Due to the fact that peak centroids are used, a binning step is not necessary. - | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals. +**PeakGroups** + | This method performs retention time adjustment based on the alignment of chromatographic peak groups present in all/most samples (hence corresponding to house keeping compounds). First the retention time deviation of these peak groups is described by fitting either a polynomial (‘smooth = "loess"’) or a linear ( ‘smooth = "linear"’) model to the data points. These models are subsequently used to adjust the retention time of each spectrum in each sample. + | See the PeakGroups_manual_ ------------- -Output files ------------- +**Obiwarp** -IPO_parameters4xcmsSet.tsv + | This method performs retention time adjustment using the Obiwarp method [Prince 2006]. It is based on the code at http://obi-warp.sourceforge.net but supports alignment of multiple samples by aligning each against a _center_ sample. The alignment is performed directly on the ‘profile-matrix’ and can hence be performed independently of the peak detection or peak grouping. + | See the Obiwarp_manual_ - | Optimal parameters for xcmsSet - +.. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2 +.. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html --------------------------------------------------- Changelog/News -------------- - +@HELP_NEWVERSION_1_10_0_0@ ]]></help>
--- a/ipo4xcmsSet.r Thu Aug 03 06:00:00 2017 -0400 +++ b/ipo4xcmsSet.r Mon Dec 16 05:26:42 2019 -0500 @@ -2,143 +2,56 @@ #Authors Gildas Le Corguille and Yann Guitton -# ----- LOG FILE ----- -log_file=file("log.txt", open = "wt") -sink(log_file) -sink(log_file, type = "output") - +# ----- PACKAGE ----- +cat("\tSESSION INFO\n") -# ----- PACKAGE ----- -options(bitmapType='cairo') -cat("\tPACKAGE INFO\n") -#pkgs=c("xcms","batch") -pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch") -for(pkg in pkgs) { - suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) - cat(pkg,"\t",as.character(packageVersion(pkg)),"\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"); +#Import the different functions +source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +source_local("lib.r") - - +pkgs <- c("IPO","batch") +loadAndDisplayPackages(pkgs) +cat("\n\n"); # ----- ARGUMENTS ----- cat("\tARGUMENTS INFO\n") -listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects -write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') +args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(args), col.names=F, quote=F, sep='\t') cat("\n\n"); - -# ----- ARGUMENTS PROCESSING ----- -cat("\tINFILE PROCESSING INFO\n") - - -#Import the different functions -source_local("lib.r") - -cat("\n\n") - -#Import the different functions - # ----- PROCESSING INFILE ----- cat("\tARGUMENTS PROCESSING INFO\n") - -xsetRdataOutput = paste("ipo4xcmsSet","RData",sep=".") -if (!is.null(listArguments[["xsetRdataOutput"]])){ - xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL -} - -parametersOutput = "parametersOutput.tsv" -if (!is.null(listArguments[["parametersOutput"]])){ - parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL -} +options(bitmapType='cairo') samplebyclass = 2 -if (!is.null(listArguments[["samplebyclass"]])){ - samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL -} - -#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_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL - singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL +if (!is.null(args$samplebyclass)){ + samplebyclass = args$samplebyclass; args$samplebyclass=NULL } -# single file case -#@TODO: need to be refactoring -if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) { - 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) - } - - cwd=getwd() - dir.create("raw") - setwd("raw") - file.symlink(singlefile_galaxyPath,singlefile_sampleName) - setwd(cwd) - - directory = "raw" - -} - -# We unzip automatically the chromatograms from the zip files. -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) - } +# ----- INFILE PROCESSING ----- +cat("\tINFILE PROCESSING INFO\n") - #list all file in the zip file - #zip_files=unzip(zipfile,list=T)[,"Name"] - - # Because IPO only want raw data in its working directory - dir.create("ipoworkingdir") - setwd("ipoworkingdir") - - #unzip - suppressWarnings(unzip(zipfile, unzip="unzip")) +# Handle infiles +if (!exists("singlefile")) singlefile <- NULL +rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args) +singlefile <- rawFilePath$singlefile +directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL) - #get the directory name - filesInZip=unzip(zipfile, list=T); - directories=unique(unlist(lapply(strsplit(filesInZip$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") - - -} - -#addition of the directory to the list of arguments in the first position +# Check some character issues checkXmlStructure(directory) -checkFilesCompatibilityWithXcms(directory) cat("\n\n") - - # ----- MAIN PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") -xset = ipo4xcmsSet(directory, parametersOutput, listArguments, samplebyclass) +xset = ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass) @@ -153,8 +66,8 @@ #saving R data in .Rdata file to save the variables used in the present tool -objects2save = c("xset","zipfile") -save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) +objects2save = c("xset", "singlefile") +save(list=objects2save[objects2save %in% ls()], file="ipo4xcmsSet.RData") cat("\n\n")
--- a/ipo4xcmsSet.xml Thu Aug 03 06:00:00 2017 -0400 +++ b/ipo4xcmsSet.xml Mon Dec 16 05:26:42 2019 -0500 @@ -1,43 +1,17 @@ -<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3"> +<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="@TOOL_VERSION@+galaxy0"> - <description>IPO optimization process for xcms.xcmsSet</description> + <description>IPO optimization process for xcms.findChromPeaks</description> <macros> <import>macros.xml</import> - - <macro name="centwave_ppm_fixed"> - <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" /> - </macro> - <macro name="centwave_peakwidth_fixed"> - <param name="min_peakwidth" type="float" value="20" label="Min peak width range in seconds" optional="true" help="[min_peakwidth]" /> - <param name="max_peakwidth" type="float" value="50" label="Max peak width range in seconds" optional="true" help="[max_peakwidth]" /> - </macro> - <macro name="centwave_mzdiff_fixed"> - <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] Can be negative to allow overlap" /> - </macro> - - <macro name="matchedfilter_fwhm_fixed"> - <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> - </macro> - <macro name="matchedfilter_mzdiff_fixed"> - <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " /> - </macro> </macros> <expand macro="requirements"/> - <expand macro="stdio"/> - - <command><![CDATA[ - LANG=C Rscript $__tool_directory__/ipo4xcmsSet.r - #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): - singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' - #else - zipfile '$input' - #end if + <command detect_errors="exit_code"><![CDATA[ + LANG=C Rscript '$__tool_directory__/ipo4xcmsSet.r' - parametersOutput $parametersOutput - xsetRdataOutput $xsetRData + singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' samplebyclass $samplebyclass @@ -45,10 +19,10 @@ @COMMAND_NSLAVES@ method $methods.method #if $methods.method == "centWave": - ppm "c($methods.section_centwave_optiomizable.conditional_parameter.ppm)" - min_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.min_peakwidth)" - max_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.max_peakwidth)" - mzdiff "c($methods.section_centwave_optiomizable.conditional_parameter.mzdiff)" + ppm "c($methods.section_centwave_optiomizable.ppm)" + min_peakwidth "c($methods.section_centwave_optiomizable.min_peakwidth)" + max_peakwidth "c($methods.section_centwave_optiomizable.max_peakwidth)" + mzdiff "c($methods.section_centwave_optiomizable.mzdiff)" snthresh $methods.section_centwave_non_optiomizable.snthresh integrate $methods.section_centwave_non_optiomizable.integrate @@ -56,26 +30,24 @@ prefilter "c($methods.section_centwave_non_optiomizable.prefilter)" #elif $methods.method == "matchedFilter": - fwhm "c($methods.section_matchedfilter_optiomizable.conditional_parameter.fwhm)" - mzdiff "c($methods.section_matchedfilter_optiomizable.conditional_parameter.mzdiff)" + fwhm "c($methods.section_matchedfilter_optiomizable.fwhm)" + mzdiff "c($methods.section_matchedfilter_optiomizable.mzdiff)" step $methods.section_matchedfilter_non_optimizable.step steps $methods.section_matchedfilter_non_optimizable.steps max $methods.section_matchedfilter_non_optimizable.max snthresh $methods.section_matchedfilter_non_optimizable.snthresh #end if - - @COMMAND_LOG_EXIT@ ]]></command> <inputs> - <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" 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." /> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. See the help section below." /> <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" /> <conditional name="methods"> - <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below"> + <param argument="method" type="select" label="Extraction method for peaks detection (findChromPeaks)" help="See the help section below"> <option value="centWave" >centWave</option> <option value="matchedFilter" selected="true">matchedFilter</option> </param> @@ -83,78 +55,47 @@ <!-- centWave Filter options --> <when value="centWave"> <section name="section_centwave_optiomizable" title="Optimizable parameters" expanded="True"> - <conditional name="conditional_parameter"> - <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> - <option value="ppm">Max tolerated ppm m/z deviation in consecutive scans in ppm [ppm]</option> - <option value="peakwidth">Min,Max peak width in seconds [peakwidth]</option> - <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option> - </param> - <when value="ppm"> - <param name="ppm" type="text" value="17,32" label="Range for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="[ppm] (ex: 25 or 17,32)"> - <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator> - </param> - <expand macro="centwave_peakwidth_fixed" /> - <expand macro="centwave_mzdiff_fixed" /> - </when> - <when value="peakwidth"> - <param name="min_peakwidth" type="text" value="12,18" label="Range for Min peak width range in seconds" optional="true" help="[min_peakwidth] (ex: 12,18)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator> - </param> - <param name="max_peakwidth" type="text" value="35,65" label="Range for Max peak width range in seconds" optional="true" help="[max_peakwidth] (ex: 35,65)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator> - </param> - <expand macro="centwave_ppm_fixed" /> - <expand macro="centwave_mzdiff_fixed" /> - </when> - <when value="mzdiff"> - <param name="mzdiff" type="text" value="-0.001,0.010" label="Range for Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap (ex: -0.001,0.010)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> - </param> - <expand macro="centwave_ppm_fixed" /> - <expand macro="centwave_peakwidth_fixed" /> - </when> - </conditional> + <param argument="ppm" type="text" value="17,32" label="Range or a fixed value for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="(ex: 25 or 17,32)"> + <expand macro="input_validator_range_integer"/> + </param> + <param argument="min_peakwidth" type="text" value="12,18" label="Range or a fixed value for Min peak width range in seconds" optional="true" help="(ex: 12,18)"> + <expand macro="input_validator_range_float"/> + </param> + <param argument="max_peakwidth" type="text" value="35,65" label="Range or a fixed value for Max peak width range in seconds" optional="true" help="(ex: 35,65)"> + <expand macro="input_validator_range_float"/> + </param> + <param argument="mzdiff" type="text" value="-0.001,0.010" label="Range or a fixed value for Minimum difference in m/z for peaks with overlapping retention times" help="Can be negative to allow overlap (ex: -0.001,0.010)"> + <expand macro="input_validator_range_float_neg"/> + </param> </section> <section name="section_centwave_non_optiomizable" title="Non optimizable parameters" expanded="True"> - <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" /> - <param name="integrate" type="select" label="Peak limits method" help="[integrate]" > + <param argument="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="Signal to noise ratio cutoff" /> + <param argument="integrate" type="select" label="Peak limits method" > <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> <option value="2">peak limits based on real data (more sensitive to noise)</option> </param> - <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> - <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> + <param argument="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> + <param argument="noise" type="integer" value="0" label="Noise filter" help="optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> </section> </when> <!-- matched Filter options --> <when value="matchedFilter"> <section name="section_matchedfilter_optiomizable" title="Optimizable parameters" expanded="True"> - <conditional name="conditional_parameter"> - <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> - <option value="fwhm">Full width at half maximum of matched filtration gaussian model peak [fwhm]</option> - <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option> - </param> - <when value="fwhm"> - <param name="fwhm" type="text" value="25,35" label="Range for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="[fwhm] Only used to calculate the actual sigma (ex: 25,35)"> - <validator type="regex" message="Should be this format: XX,YY">[0-9]+,[0-9]+</validator> - </param> - <expand macro="matchedfilter_mzdiff_fixed" /> - </when> - <when value="mzdiff"> - <param name="mzdiff" type="text" value="0.4,0.7" label="Range for Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps (ex: 0.4,0.7)"> - <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> - </param> - <expand macro="matchedfilter_fwhm_fixed" /> - </when> - </conditional> + <param argument="fwhm" type="text" value="25,35" label="Range or a fixed value for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="Only used to calculate the actual sigma (ex: 25,35)"> + <expand macro="input_validator_range_integer"/> + </param> + <param argument="mzdiff" type="text" value="0.4,0.7" label="Range or a fixed value for Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-step*steps (ex: 0.4,0.7)"> + <expand macro="input_validator_range_float_neg"/> + </param> </section> <section name="section_matchedfilter_non_optimizable" title="Non optimizable parameters" expanded="True"> - <param name="step" type="float" value="0.1" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> - <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> - <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" /> - <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" /> + <param argument="step" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> + <param argument="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> + <param argument="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" /> + <param argument="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" /> </section> </when> </conditional> @@ -163,9 +104,8 @@ </inputs> <outputs> - <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" /> - <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" /> - <data name="log" format="txt" label="ipo4xcmsSet.log.txt" /> + <data name="xsetRData" format="rdata.xcms.raw" label="ipo4xcmsSet.RData" from_work_dir="ipo4xcmsSet.RData" /> + <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" from_work_dir="IPO_parameters4xcmsSet.tsv" /> </outputs> <tests> @@ -175,13 +115,10 @@ <conditional name="methods"> <param name="method" value="centWave" /> <section name="section_centwave_optiomizable" > - <conditional name="conditional_parameter"> - <param name="select_parameter" value="peakwidth" /> - <param name="min_peakwidth" value="3,9.5" /> - <param name="max_peakwidth" value="10,20" /> - <param name="ppm" value="56" /> - <param name="mzdiff" value="-0.001" /> - </conditional> + <param name="min_peakwidth" value="3,9.5" /> + <param name="max_peakwidth" value="10,20" /> + <param name="ppm" value="56" /> + <param name="mzdiff" value="-0.001" /> </section> </conditional> <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_peakwidth.tsv" /> @@ -192,51 +129,29 @@ <conditional name="methods"> <param name="method" value="centWave" /> <section name="section_centwave_optiomizable" > - <conditional name="conditional_parameter"> - <param name="select_parameter" value="ppm" /> - <param name="ppm" value="50,60" /> - <param name="min_peakwidth" value="3.325" /> - <param name="max_peakwidth" value="11" /> - <param name="mzdiff" value="-0.001" /> - </conditional> + <param name="ppm" value="50,60" /> + <param name="min_peakwidth" value="3.325" /> + <param name="max_peakwidth" value="11.0" /> + <param name="mzdiff" value="-0.001" /> </section> </conditional> - <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_ppm.tsv" /> + <output name="parametersOutput"> + <assert_contents> + <!-- 	 is XML escape code for tab --> + <has_line line="ppm	60" /> + <has_line line="min_peakwidth	3.325" /> + <has_line line="max_peakwidth	11" /> + <has_line line="mzdiff	-0.001" /> + <has_line line="prefilter	3" /> + <has_line line="snthresh	10" /> + <has_line line="integrate	1" /> + <has_line line="noise	0" /> + <has_line line="value_of_prefilter	100" /> + <has_line line="mzCenterFun	wMean" /> + <has_line line="fitgauss	FALSE" /> + </assert_contents> + </output> </test> - <!-- Too long for Travis CI --> - <!--<test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" /> - <param name="samplebyclass" value="1" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="25" /> - <param name="methods|min_peakwidth" value="20,30" /> - <param name="methods|max_peakwidth" value="45,55" /> - <output name="parametersOutput" file="sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv" /> - </test>--> - <!-- Too long for Travis CI --> - <!--<test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" /> - <param name="samplebyclass" value="1" /> - <param name="methods|method" value="matchedFilter" /> - <param name="methods|step" value="0.05,0.15" /> - <param name="methods|fwhm" value="25,35" /> - <output name="parametersOutput" file="sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv" /> - </test>--> - <!--Failed: - Error in resultIncreased(history) : - No isotopes have been detected, peak picking not optimizable by IPO!--> - <!--<test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="25" /> - <param name="methods|min_peakwidth" value="15,25" /> - <param name="methods|min_peakwidth" value="20,30" /> - <param name="methods|max_peakwidth" value="45,55" /> - <output name="parametersOutput" file="faahKO_IPO_parameters4xcmsSet.tsv" /> - </test>--> </tests> <help><![CDATA[ @@ -260,11 +175,13 @@ **Upstream tools** -========================= ================= ======= ========= -Name output file format parameter -========================= ================= ======= ========= -NA NA zip NA -========================= ================= ======= ========= +========================= ======================== +Name Format +========================= ======================== +Upload File mzxml,mzml,mzdata,netcdf +========================= ======================== + +The easier way to process is to create a Dataset Collection of the type List **Downstream tools** @@ -281,43 +198,6 @@ Input files ----------- -+---------------------------+------------+ -| Parameter : num + label | Format | -+===========================+============+ -| 1 : Choose your inputs | zip | -+---------------------------+------------+ - -**Choose your inputs** - -You have two methods for your inputs: - - | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). - | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories. - -Steps for creating the zip file -------------------------------- - -**Step1: Creating your directory and hierarchize the subdirectories** - - -VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug). - -Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild): -arabidopsis/wild/01.raw -arabidopsis/mutant/01.raw - -**Step2: Creating a zip file** - -Create your zip file (e.g.: arabidopsis.zip). - -**Step 3 : Uploading it to our Galaxy server** - -If your zip file is less than 2Gb, you get use the Get Data tool to upload it. - -Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf). - -For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org). - Advices for converting your files for the XCMS input ---------------------------------------------------- @@ -344,37 +224,30 @@ Parameters ---------- -Extraction method for peaks detection +Extraction method for findChromPeaks ------------------------------------- -**Matched Filter** - - | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. - | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002). +**MatchedFilter** + | The matchedFilter algorithm identifies peaks in the chromatographic time domain as described in [Smith 2006]. The intensity values are binned by cutting The LC/MS data into slices (bins) of a mass unit (‘binSize’ m/z) wide. Within each bin the maximal intensity is selected. The chromatographic peak detection is then performed in each bin by extending it based on the ‘steps’ parameter to generate slices comprising bins ‘current_bin - steps +1’ to ‘current_bin + steps - 1’. Each of these slices is then filtered with matched filtration using a second-derative Gaussian as the model peak shape. After filtration peaks are detected using a signal-to-ratio cut-off. For more details and illustrations see [Smith 2006]. + | See the MatchedFilter_manual_ -**cent Wave** +**CentWave** - | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode. + | The centWave algorithm perform peak density and wavelet based chromatographic peak detection for high resolution LC/MS data in centroid mode [Tautenhahn 2008]. | Due to the fact that peak centroids are used, a binning step is not necessary. | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals. - + | See the CentWave_manual_ ------------- -Output files ------------- - -IPO_parameters4xcmsSet.tsv - - | Optimal parameters for xcmsSet - +.. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2 +.. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2 --------------------------------------------------- Changelog/News -------------- - +@HELP_NEWVERSION_1_10_0_0@ ]]></help>
--- a/lib.r Thu Aug 03 06:00:00 2017 -0400 +++ b/lib.r Mon Dec 16 05:26:42 2019 -0500 @@ -1,11 +1,37 @@ +#@author G. Le Corguille +# solve an issue with batch if arguments are logical TRUE/FALSE +parseCommandArgs <- function(...) { + args <- batch::parseCommandArgs(...) + for (key in names(args)) { + if (args[key] %in% c("TRUE","FALSE")) + args[key] = as.logical(args[key]) + } + return(args) +} + +#@author G. Le Corguille +# This function will +# - load the packages +# - display the sessionInfo +loadAndDisplayPackages <- function(pkgs) { + for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + sessioninfo = sessionInfo() + cat(sessioninfo$R.version$version.string,"\n") + cat("Main packages:\n") + for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + cat("Other loaded packages:\n") + for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") +} + ## ## This function launch IPO functions to get the best parameters for xcmsSet ## A sample among the whole dataset is used to save time ## -ipo4xcmsSet = function(directory, parametersOutput, listArguments, samplebyclass=4) { +ipo4xcmsSet = function(directory, parametersOutput, args, samplebyclass=4) { setwd(directory) files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF" + files = files[!files %in% c("conda_activate.log", "log.txt")] files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT" mzmlfile = files @@ -27,14 +53,13 @@ cat("\t\tSamples used:\n") print(mzmlfile) - peakpickingParameters = getDefaultXcmsSetStartingParams(listArguments[["method"]]) #get default parameters of IPO + peakpickingParameters = getDefaultXcmsSetStartingParams(args$method) #get default parameters of IPO - # filter listArguments to only get releavant parameters and complete with those that are not declared - peakpickingParametersUser = c(listArguments[names(listArguments) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(listArguments))]) + # filter args to only get releavant parameters and complete with those that are not declared + peakpickingParametersUser = c(args[names(args) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(args))]) peakpickingParametersUser$verbose.columns = TRUE - #peakpickingParametersUser$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement - resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves=peakpickingParametersUser$nSlaves, subdir="../IPO_results") #some images generated by IPO + resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves=args$nSlaves, subdir="../IPO_results") #some images generated by IPO # export resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))] @@ -46,19 +71,20 @@ ## ## This function launch IPO functions to get the best parameters for group and retcor ## -ipo4retgroup = function(xset, directory, parametersOutput, listArguments, samplebyclass=4) { +ipo4retgroup = function(xset, directory, parametersOutput, args, samplebyclass=4) { setwd(directory) files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF" + files = files[!files %in% c("conda_activate.log", "log.txt")] files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT" - retcorGroupParameters = getDefaultRetGroupStartingParams(listArguments[["retcorMethod"]]) #get default parameters of IPO + retcorGroupParameters = getDefaultRetGroupStartingParams(args$retcorMethod) #get default parameters of IPO print(retcorGroupParameters) - # filter listArguments to only get releavant parameters and complete with those that are not declared - retcorGroupParametersUser = c(listArguments[names(listArguments) %in% names(retcorGroupParameters)], retcorGroupParameters[!(names(retcorGroupParameters) %in% names(listArguments))]) + # filter args to only get releavant parameters and complete with those that are not declared + retcorGroupParametersUser = c(args[names(args) %in% names(retcorGroupParameters)], retcorGroupParameters[!(names(retcorGroupParameters) %in% names(args))]) print("retcorGroupParametersUser") print(retcorGroupParametersUser) - resultRetcorGroup = optimizeRetGroup(xset, retcorGroupParametersUser, nSlaves=listArguments[["nSlaves"]], subdir="../IPO_results") #some images generated by IPO + resultRetcorGroup = optimizeRetGroup(xset, retcorGroupParametersUser, nSlaves=args$nSlaves, subdir="../IPO_results") #some images generated by IPO # export resultRetcorGroup_best_settings_parameters = resultRetcorGroup$best_settings @@ -67,48 +93,13 @@ - -## -## This function check if xcms will found all the files -## -#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM -checkFilesCompatibilityWithXcms <- function(directory) { - cat("Checking files filenames compatibilities with xmcs...\n") - # WHAT XCMS WILL FIND - filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") - filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") - info <- file.info(directory) - listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) - files <- c(directory[!info$isdir], listed) - files_abs <- file.path(getwd(), files) - exists <- file.exists(files_abs) - files[exists] <- files_abs[exists] - files[exists] <- sub("//","/",files[exists]) - - # WHAT IS ON THE FILESYSTEM - filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) - filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] - - # COMPARISON - if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { - write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) - write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) - stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") - - } -} - - - -## -## This function check if XML contains special caracters. It also checks integrity and completness. -## +# This function check if XML contains special caracters. It also checks integrity and completness. #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM checkXmlStructure <- function (directory) { cat("Checking XML structure...\n") - cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") - capture=system(cmd,intern=TRUE) + cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") + capture <- system(cmd, intern=TRUE) if (length(capture)>0){ #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) @@ -118,3 +109,96 @@ } } + + +# This function get the raw file path from the arguments +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") { + if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") + + if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]] + + if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { + singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]] + singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]] + } + 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] + # In case, an url is used to import data within Galaxy + singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) + singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath + } + } + return(list(zipfile=zipfile, singlefile=singlefile)) +} + +# 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 +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +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) + } + + if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) + file.copy(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 + suppressWarnings(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)$isdir] + directory <- "." + if (length(directories) == 1) directory <- directories + + cat("files_root_directory\t",directory,"\n") + + } + return (directory) +} + + +# This function retrieve a xset like object +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + if (!is.null(xset@phenoData$sample_group)) + sampclass(xset) <- xset@phenoData$sample_group + else + sampclass(xset) <- "." + return (xset) + } +}
--- a/macros.xml Thu Aug 03 06:00:00 2017 -0400 +++ b/macros.xml Mon Dec 16 05:26:42 2019 -0500 @@ -1,74 +1,58 @@ <?xml version="1.0"?> <macros> + <token name="@TOOL_VERSION@">1.10.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4_1">r-snow</requirement> - <requirement type="package" version="1.0.0">bioconductor-ipo</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-ipo</requirement> + <requirement type="package" version="1.1_5">r-batch</requirement> </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code range="1" level="fatal" /> - </stdio> - </xml> - <token name="@COMMAND_SCRIPT@"> - LANG=C Rscript $__tool_directory__/ - </token> - - <token name="@COMMAND_LOG_EXIT@"> - ; - return=\$?; - mv log.txt $log; - cat $log; - sh -c "exit \$return" - </token> - - <token name="@COMMAND_NSLAVES@"> + <token name="@COMMAND_NSLAVES@"><![CDATA[ nSlaves \${GALAXY_SLOTS:-1} - </token> + ]]></token> <!-- zipfile load for planemo test --> - <token name="@COMMAND_FILE_LOAD@"> + <token name="@ESCAPE_IDENTIFIER@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($single_file.element_identifier))]]></token> + <token name="@COMMAND_FILE_LOAD@"><![CDATA[ + #import re #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 ] ) + #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = '|'.join( ["%s" % re.sub('[^\s\w\-\.]', '_', str($single_file.element_identifier)) for single_file in $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #end if + ]]></token> - singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' - #else - zipfile '$file_load_section.file_load_conditional.input' - #end if - #end if - </token> + <xml name="input_validator_range_integer"> + <validator type="regex" message="Should be this format: XX or XX,YY">[0-9]+,?[0-9]*</validator> + </xml> + + <xml name="input_validator_range_float"> + <validator type="regex" message="Should be one combinaison of those format: XX, XX.YY, XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,?[0-9]*[\.]?[0-9]*</validator> + </xml> + + <xml name="input_validator_range_float_neg"> + <validator type="regex" message="Should be one combinaison of those format: XX, XX.YY, XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,?[\-]?[0-9]*[\.]?[0-9]*</validator> + </xml> <xml name="input_file_load"> - <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> + <section name="file_load_section" title="Resubmit your raw dataset"> <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." > + <param name="file_load_select" type="select" label="Resubmit your dataset" help="Use only if you get a message which say that your original dataset 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." /> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf" 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"> @@ -78,7 +62,7 @@ </section> </xml> - <token name="@HELP_AUTHORS@"> + <token name="@HELP_AUTHORS@"><![CDATA[ .. class:: infomark **Authors** Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes @@ -91,7 +75,12 @@ --------------------------------------------------- - </token> + ]]></token> + <token name="@HELP_NEWVERSION_1_10_0_0@"><![CDATA[ +**Version 1.10.0+galaxy0 - 03/09/2019** + +- NEW: new versions of the IPO wrappers based on IPO-1.10.0 + ]]></token> <xml name="citation">
--- a/planemo_test.sh Thu Aug 03 06:00:00 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -conda create -n r-ipo --use-local r-ipo r-batch -. ~/miniconda2/bin/activate r-ipo -planemo test --install_galaxy --galaxy_branch "dev" --update_test_data - - -# -- Use of conda dependencies -planemo conda_init --conda_prefix /tmp/mc -planemo conda_install --conda_prefix /tmp/mc . -planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution - -planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --conda_prefix /tmp/mc --galaxy_branch dev > planemo.out 2>&1
--- a/repository_dependencies.xml Thu Aug 03 06:00:00 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories> - <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories>
--- a/test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv Thu Aug 03 06:00:00 2017 -0400 +++ b/test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv Mon Dec 16 05:26:42 2019 -0500 @@ -1,8 +1,8 @@ ppm 60 -prefilter 3 min_peakwidth 3.325 max_peakwidth 11 mzdiff -0.001 +prefilter 3 snthresh 10 integrate 1 noise 0
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--- a/test-data/MM_IPO_parameters4retgroup.tsv Thu Aug 03 06:00:00 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -""
--- a/test-data/faahKO_IPO_parameters4retgroup_bw.tsv Thu Aug 03 06:00:00 2017 -0400 +++ b/test-data/faahKO_IPO_parameters4retgroup_bw.tsv Mon Dec 16 05:26:42 2019 -0500 @@ -1,5 +1,5 @@ -bw 4.168192 -mzwid 0.25 +bw 5.5 +mzwid 0.02 minfrac 1 max 50 retcorMethod loess
--- a/test-data/sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv Thu Aug 03 06:00:00 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -"min_peakwidth" "max_peakwidth" "mzdiff" "ppm" "snthresh" "noise" "prefilter" "value_of_prefilter" "mzCenterFun" "integrate" "fitgauss" -7.5 42.5 0.01715 25 10 0 3 100 "wMean" 1 FALSE