Mercurial > repos > lecorguille > xcms_xcmsset
changeset 37:9ada611dd63f draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
| author | lecorguille |
|---|---|
| date | Fri, 31 Aug 2018 08:59:03 -0400 |
| parents | d39b9aff9cf7 |
| children | e66eeca443e4 |
| files | abims_xcms_xcmsSet.xml lib.r test-data/faahKO.raw.RData test-data/faahKO.raw.Rdata test-data/ko15-raw.RData test-data/ko15-raw.Rdata test-data/ko16-raw.Rdata test-data/ko16.CDF test-data/wt15-raw.Rdata test-data/wt15.CDF test-data/wt16-raw.Rdata test-data/wt16.CDF xcms_xcmsSet.r |
| diffstat | 13 files changed, 67 insertions(+), 65 deletions(-) [+] |
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--- a/abims_xcms_xcmsSet.xml Thu Apr 05 18:05:45 2018 -0400 +++ b/abims_xcms_xcmsSet.xml Fri Aug 31 08:59:03 2018 -0400 @@ -46,14 +46,14 @@ #elif $methods.method == "MatchedFilter": fwhm $methods.fwhm binSize $methods.binSize - impute $methods.impute_cond.impute - #if $methods.impute_cond.impute == "linbase": - #if $methods.impute_cond.baseValue != "": - baseValue $methods.impute_cond.baseValue + ## Advanced + impute $methods.MatchedFilterAdv.impute_cond.impute + #if $methods.MatchedFilterAdv.impute_cond.impute == "linbase": + #if $methods.MatchedFilterAdv.impute_cond.baseValue != "": + baseValue $methods.MatchedFilterAdv.impute_cond.baseValue #end if - distance $methods.impute_cond.distance + distance $methods.MatchedFilterAdv.impute_cond.distance #end if - ## Advanced #if $methods.MatchedFilterAdv.sigma != "": sigma $methods.MatchedFilterAdv.sigma #end if @@ -113,22 +113,22 @@ <when value="MatchedFilter"> <param argument="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="Only used to calculate the actual sigma" /> <param argument="binSize" 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. (Previously step)" /> - <conditional name="impute_cond"> - <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)"> - <option value="none">none - no linear interpolation</option> - <option value="lin">lin - linear interpolation</option> - <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option> - <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option> - </param> - <when value="none" /> - <when value="lin" /> - <when value="linbase"> - <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." /> - <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." /> - </when> - <when value="intlin" /> - </conditional> <section name="MatchedFilterAdv" title="Advanced Options" expanded="False"> + <conditional name="impute_cond"> + <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)"> + <option value="none">none - no linear interpolation</option> + <option value="lin">lin - linear interpolation</option> + <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option> + <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option> + </param> + <when value="none" /> + <when value="lin" /> + <when value="linbase"> + <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." /> + <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." /> + </when> + <when value="intlin" /> + </conditional> <param argument="sigma" type="float" value="" optional="true" label="Standard deviation (width) of matched filtration model peak" help="Leave it to empty to calculate it using fwhm by default at fwhm/2.3548" /> <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" /> <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" /> @@ -218,7 +218,7 @@ </assert_stdout> </test>--> <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -237,9 +237,9 @@ </assert_stdout> </test> <!-- DISABLE FOR TRAVIS - Useful to generate test-data for the further steps --> + Useful to generate test-data for the further steps <test> - <param name="image" value="ko16-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko16-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -255,7 +255,7 @@ </assert_stdout> </test> <test> - <param name="image" value="wt15-raw.Rdata" ftype="rdata" /> + <param name="image" value="wt15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -271,7 +271,7 @@ </assert_stdout> </test> <test> - <param name="image" value="wt16-raw.Rdata" ftype="rdata" /> + <param name="image" value="wt16-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -286,19 +286,21 @@ <has_text text="Sample classes: ." /> </assert_stdout> </test> - + --> <!-- DISABLE FOR TRAVIS Test to test the different methods parameters <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="MatchedFilter" /> <param name="fwhm" value="35" /> - <conditional name="impute_cond"> - <param name="impute" value="linbase" /> - <param name="baseValue" value="0.1" /> - <param name="distance" value="1" /> - </conditional> + <section name="MatchedFilterAdv" + <conditional name="impute_cond"> + <param name="impute" value="linbase" /> + <param name="baseValue" value="0.1" /> + <param name="distance" value="1" /> + </conditional> + </section> </conditional> <assert_stdout> <has_text text="fwhm: 35" /> @@ -308,7 +310,7 @@ </assert_stdout> </test> <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWavePredIso" /> <param name="ppm" value="56" /> @@ -323,7 +325,7 @@ </assert_stdout> </test> <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="MSW" /> <param name="snthresh" value="4" /> @@ -479,7 +481,7 @@ xset.RData: rdata.xcms.findchrompeaks format - | Rdata file that is necessary in the second step of the workflow "xcms.group". + | RData file that is necessary in the second step of the workflow "xcms.group". ---------------------------------------------------
--- a/lib.r Thu Apr 05 18:05:45 2018 -0400 +++ b/lib.r Fri Aug 31 08:59:03 2018 -0400 @@ -391,38 +391,31 @@ # This function get the raw file path from the arguments #@author Gildas Le Corguille lecorguille@sb-roscoff.fr -getRawfilePathFromArguments <- function(singlefile, zipfile, args) { - if (!is.null(args$zipfile)) zipfile <- args$zipfile - if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive - if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative +getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") { + if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") + + if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]] - if (!is.null(args$singlefile_galaxyPath)) { - singlefile_galaxyPaths <- args$singlefile_galaxyPath; - singlefile_sampleNames <- args$singlefile_sampleName - } - if (!is.null(args$singlefile_galaxyPathPositive)) { - singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive; - singlefile_sampleNames <- args$singlefile_sampleNamePositive + if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { + singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]] + singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]] + } + if (exists("singlefile_galaxyPaths")){ + singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|")) + singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|")) + + singlefile <- NULL + for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { + singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] + singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] + # In case, an url is used to import data within Galaxy + singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) + singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath } - if (!is.null(args$singlefile_galaxyPathNegative)) { - singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative; - singlefile_sampleNames <- args$singlefile_sampleNameNegative - } - if (exists("singlefile_galaxyPaths")){ - singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|")) - singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|")) - - singlefile <- NULL - for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { - singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] - singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] - singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath - } - } - return(list(zipfile=zipfile, singlefile=singlefile)) + } + 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 @@ -480,7 +473,10 @@ if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object suppressWarnings(xset <- as(xobject, 'xcmsSet')) - sampclass(xset) <- xset@phenoData$sample_group + if (!is.null(xset@phenoData$sample_group)) + sampclass(xset) <- xset@phenoData$sample_group + else + sampclass(xset) <- "." return (xset) } }
--- a/xcms_xcmsSet.r Thu Apr 05 18:05:45 2018 -0400 +++ b/xcms_xcmsSet.r Fri Aug 31 08:59:03 2018 -0400 @@ -83,6 +83,10 @@ if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2]) if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam) if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam) +#Apply this filter only if file contain MS and MSn +if(length(unique(msLevel(raw_data)))!= 1){ + raw_data <- filterMsLevel(raw_data,msLevel=1) +} cat("\t\t\tChromatographic peak detection\n") # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...