Mercurial > repos > lecorguille > ipo
changeset 4:9fa5856f6184 draft
planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62
| author | lecorguille |
|---|---|
| date | Thu, 28 Jul 2016 11:11:38 -0400 |
| parents | 9f1e18bc8ce3 |
| children | d63c80d54b24 |
| files | ipo.r ipo4xcmsSet.xml lib.r macros.xml planemo_test.sh test-data/MM14_IPO_parameters4xcmsSet.tsv test-data/sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv test-data/sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv |
| diffstat | 8 files changed, 96 insertions(+), 36 deletions(-) [+] |
line wrap: on
line diff
--- a/ipo.r Thu Jul 28 11:03:04 2016 -0400 +++ b/ipo.r Thu Jul 28 11:11:38 2016 -0400 @@ -11,7 +11,7 @@ # ----- PACKAGE ----- cat("\tPACKAGE INFO\n") #pkgs=c("xcms","batch") -pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","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="")
--- a/ipo4xcmsSet.xml Thu Jul 28 11:03:04 2016 -0400 +++ b/ipo4xcmsSet.xml Thu Jul 28 11:11:38 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="2.0.8"> +<tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3"> <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> @@ -25,12 +25,27 @@ ## profmethod $profmethod nSlaves \${GALAXY_SLOTS:-1} method $methods.method #if $methods.method == "centWave": - ppm $methods.ppm + ppm "c($methods.ppm)" min_peakwidth "c($methods.min_peakwidth)" max_peakwidth "c($methods.max_peakwidth)" + #if $methods.options_c.option == "show": + mzdiff "c($methods.options_c.mzdiff)" + snthresh "c($methods.options_c.snthresh)" + integrate "c($methods.options_c.integrate)" + noise "c($methods.options_c.noise)" + prefilter "c($methods.options_c.prefilter)" + prefilter_value "c($methods.options_c.prefilter_value)" + #end if #elif $methods.method == "matchedFilter": - step $methods.step - fwhm $methods.fwhm + step "c($methods.step)" + fwhm "c($methods.fwhm)" + #if $methods.options_m.option == "show": + sigma "c($methods.options_m.sigma)" + max "c($methods.options_m.max)" + snthresh "c($methods.options_m.snthresh)" + mzdiff "c($methods.options_m.mzdiff)" + steps "c($methods.options_m.steps)" + #end if #end if @COMMAND_LOG_EXIT@ 2> /tmp/log.err @@ -61,15 +76,47 @@ <!-- centWave Filter options --> <when value="centWave"> - <param name="ppm" type="text" value="5,25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" optional="false" /> - <param name="min_peakwidth" type="text" value="15,25" label="Min peak width range in seconds" help="[peakwidth]" optional="true" /> - <param name="max_peakwidth" type="text" value="45,55" label="Max peak width range in seconds" help="[peakwidth]" optional="true" /> + <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)" /> + <param name="min_peakwidth" type="text" value="15,25" label="Range for Min peak width range in seconds" optional="true" help="[min_peakwidth] (ex: 20 or 12,18)" /> + <param name="max_peakwidth" type="text" value="45,55" label="Range for Max peak width range in seconds" optional="true" help="[max_peakwidth] (ex: 50 or 35,65)" /> + <conditional name="options_c"> + <param name="option" type="select" label="Advanced options" > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="snthresh" type="text" value="10" label="Range for Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff (ex: 10 or 5,15)" /> + <param name="mzdiff" type="text" value="-0.001" label="Range for Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT (ex: -0.001 or -0.001,0.010)" /> + <param name="integrate" type="select" label="Peak limits method" help="[integrate]" multiple="true" > + <option value="1">1 - peak limits based on smoothed 2nd derivative (less precise)</option> + <option value="2">2 - peak limits based on real data (more sensitive to noise)</option> + </param> + <param name="prefilter" type="text" value="3" label="Range for the k value for the Prefilter step for the first phase" help="[prefilter] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 3 or 2,3)"/> + <param name="prefilter_value" type="text" value="100" label="Range for the I value for the Prefilter step for the first phase" help="[prefilter_value] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 100 or 95,105)"/> + <param name="noise" type="text" value="0" label="Range for the 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 (ex: 0 or 0,0.1)"/> + </when> + <when value="hide" /> + </conditional> </when> <!-- matched Filter options --> <when value="matchedFilter"> - <param name="step" type="float" value="0.01" 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" optional="true" /> - <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" optional="true" /> + <param name="step" type="text" value="0.1" label="Range for Step size to use for profile generation" optional="true" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size (ex: 0 or 0.05,0.15)" /> + <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: 30 or 25,35)" /> + <conditional name="options_m"> + <param name="option" type="select" label="Advanced options" > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="sigma" type="text" value="0" label="sigma" help="Range for standard deviation (fwhm/2.3548) (ex: 0 or 0,1)" /> + <param name="max" type="text" value="5" label="Range for Maximum number of peaks per extracted ion chromatogram" help="[max] (ex: 5 or 4,6)" /> + <param name="snthresh" type="text" value="10" label="Range for Signal to noise ratio cutoff" help="[snthresh] (ex: 10 or 3,17)" /> + <param name="steps" type="text" value="2" label="Range for 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 (ex: 2 or 1,3)" /> + <param name="mzdiff" type="text" value="0" label="m/z difference" help="Range for min m/z difference for peaks with overlapping RT (0.8-step*steps) (ex: 2 or 1,3)" /> + </when> + <when value="hide" /> + </conditional> </when> </conditional> @@ -85,15 +132,14 @@ <test> <param name="inputs|input" value="single_file" /> <param name="inputs|single_file" value="MM14.mzML" ftype="mzxml" /> + <param name="samplebyclass" value="0" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="56" /> <param name="methods|min_peakwidth" value="3,9.5" /> <param name="methods|max_peakwidth" value="10,20" /> <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet.tsv" /> </test> - <!--Failed: - Error in resultIncreased(history) : - No isotopes have been detected, peak picking not optimizable by IPO!--> + <!-- Too long for Travis CI --> <!--<test> <param name="inputs|input" value="zip_file" /> <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" /> @@ -110,10 +156,23 @@ <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="0.01" /> - <param name="methods|fwhm" value="4" /> + <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[
--- a/lib.r Thu Jul 28 11:03:04 2016 -0400 +++ b/lib.r Thu Jul 28 11:11:38 2016 -0400 @@ -4,7 +4,7 @@ ## ipo4xcmsSet = function(directory, parametersOutput, listArguments, samplebyclass=4) { setwd(directory) - #@TODO: check the behaviour of direcory = "." ? + files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF" files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT" @@ -22,22 +22,23 @@ } } } - #TODO: else, must we keep the RData to been use directly by group? + #@TODO: else, must we keep the RData to been use directly by group? cat("\t\tSamples used:\n") print(mzmlfile) - paramsPP <- getDefaultXcmsSetStartingParams(listArguments[["method"]]) #load default parameters of IPO + peakpickingParameters = getDefaultXcmsSetStartingParams(listArguments[["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))]) + peakpickingParametersUser$verbose.columns = TRUE - #user defined new parameters - paramsPP$ppm <- listArguments[["ppm"]] - paramsPP$min_peakwidth <- listArguments[["min_peakwidth"]] - paramsPP$max_peakwidth <- listArguments[["max_peakwidth"]] - paramsPP$nSlaves <- listArguments[["nSlaves"]] + #peakpickingParametersUser$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement + resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, subdir="IPO_results") #some images generated by IPO - #paramsPP$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement - resultPPpos <- optimizeXcmsSet(mzmlfile, paramsPP, subdir="IPO_results") #some images generated by IPO - write.table(resultPPpos$best_settings$parameters, file=parametersOutput, sep="\t",row.names=FALSE) #can be read by user + # export + resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))] + write.table(resultPeakpicking_best_settings_parameters, file=parametersOutput, sep="\t",row.names=FALSE) #can be read by user }
--- a/macros.xml Thu Jul 28 11:03:04 2016 -0400 +++ b/macros.xml Thu Jul 28 11:11:38 2016 -0400 @@ -2,9 +2,9 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="1.7.5">r-ipo</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.7.5">r-ipo</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> </xml> <xml name="stdio">
--- a/planemo_test.sh Thu Jul 28 11:03:04 2016 -0400 +++ b/planemo_test.sh Thu Jul 28 11:11:38 2016 -0400 @@ -6,4 +6,4 @@ # -- 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 --update_test_data +planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution
--- a/test-data/MM14_IPO_parameters4xcmsSet.tsv Thu Jul 28 11:03:04 2016 -0400 +++ b/test-data/MM14_IPO_parameters4xcmsSet.tsv Thu Jul 28 11:11:38 2016 -0400 @@ -1,2 +1,2 @@ -"min_peakwidth" "max_peakwidth" "mzdiff" "ppm" "snthresh" "noise" "prefilter" "value_of_prefilter" "mzCenterFun" "integrate" "fitgauss" "verbose.columns" "nSlaves" -5.275 13.5 0.01 56 10 0 3 100 "wMean" 1 FALSE FALSE 1 +"min_peakwidth" "max_peakwidth" "mzdiff" "ppm" "snthresh" "noise" "prefilter" "value_of_prefilter" "mzCenterFun" "integrate" "fitgauss" +5.275 13.5 0.01 56 10 0 3 100 "wMean" 1 FALSE
--- a/test-data/sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv Thu Jul 28 11:03:04 2016 -0400 +++ b/test-data/sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv Thu Jul 28 11:11:38 2016 -0400 @@ -1,2 +1,2 @@ -"min_peakwidth" "max_peakwidth" "mzdiff" "ppm" "snthresh" "noise" "prefilter" "value_of_prefilter" "mzCenterFun" "integrate" "fitgauss" "verbose.columns" "nSlaves" -7.5 42.5 0.01715 25 10 0 3 100 "wMean" 1 FALSE FALSE 1 +"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
--- a/test-data/sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv Thu Jul 28 11:03:04 2016 -0400 +++ b/test-data/sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv Thu Jul 28 11:11:38 2016 -0400 @@ -1,2 +1,2 @@ -"fwhm" "snthresh" "step" "steps" "sigma" "max" "mzdiff" "index" "nSlaves" -25 3 0.15 2.5 10.6166128758281 5 0.425 FALSE 1 +"step" "fwhm" "snthresh" "steps" "sigma" "max" "mzdiff" "index" +0.15 25 3 2.5 10.6166128758281 5 0.425 FALSE