| Previous changeset 15:6139bfcc95cb (2018-03-01) Next changeset 17:73d82de36369 (2018-10-09) |
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Commit message:
planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc |
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modified:
CAMERA.r README.rst abims_CAMERA_annotateDiffreport.xml lib.r macros.xml repository_dependencies.xml |
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added:
test-data/.RData test-data/CMD.mac.sh test-data/Rplots.pdf test-data/dataMatrixOutput.txt test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix-xcms3.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv |
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| diff -r 6139bfcc95cb -r a2c49996603e CAMERA.r --- a/CAMERA.r Thu Mar 01 08:29:32 2018 -0500 +++ b/CAMERA.r Wed Sep 19 03:22:21 2018 -0400 |
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| @@ -4,16 +4,18 @@ # ----- PACKAGE ----- -cat("\tPACKAGE INFO\n") +cat("\tSESSION INFO\n") -setRepositories(graphics=F, ind=31) +pkgs=c("CAMERA","multtest","batch") +for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) -#pkgs=c("xcms","batch") -pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch") -for(p in pkgs) { - suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) - cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") -} +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") + 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"); @@ -105,9 +107,13 @@ directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) } +# Because so far CAMERA isn't compatible with the new XCMSnExp object +if (exists("xdata")){ + xset <- getxcmsSetObject(xdata) +} -#addition of xset object to the list of arguments in the first position -if (exists("xset") != 0){ +# addition of xset object to the list of arguments in the first position +if (exists("xset")){ listArguments=append(list(xset), listArguments) } @@ -122,7 +128,6 @@ #change the default display settings pdf(file=rplotspdf, width=16, height=12) - if (thefunction %in% c("annotatediff")) { results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput) xa=results_list[["xa"]] |
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| diff -r 6139bfcc95cb -r a2c49996603e README.rst --- a/README.rst Thu Mar 01 08:29:32 2018 -0500 +++ b/README.rst Wed Sep 19 03:22:21 2018 -0400 |
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| @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 2.2.3 - 30/04/2018** + +- NEW: support the new xcms 3.0.0 wrapper + **Version 2.2.2 - 01/03/2018** - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 |
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| diff -r 6139bfcc95cb -r a2c49996603e abims_CAMERA_annotateDiffreport.xml --- a/abims_CAMERA_annotateDiffreport.xml Thu Mar 01 08:29:32 2018 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Wed Sep 19 03:22:21 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.2"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.3"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> @@ -191,14 +191,14 @@ </outputs> <tests> - <test> + <!--<test> <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> <expand macro="test_annotate_diffreport"/> <expand macro="test_annotate_quick_true"/> <expand macro="test_file_load_zip"/> <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> - </test> + </test>--> <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> <expand macro="test_annotate_diffreport"/> @@ -208,6 +208,14 @@ <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> </test> <test> + <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData"/> + <expand macro="test_annotate_diffreport"/> + <expand macro="test_annotate_quick_true"/> + <expand macro="test_file_load_single"/> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv" /> + <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix-xcms3.tsv" /> + </test> + <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> <expand macro="test_annotate_diffreport"/> <conditional name="quick_block"> @@ -424,6 +432,10 @@ Changelog/News -------------- +**Version 2.2.3 - 30/04/2018** + +- NEW: support the new xcms 3.0.0 wrapper + **Version 2.2.2 - 01/03/2018** - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 |
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| diff -r 6139bfcc95cb -r a2c49996603e lib.r --- a/lib.r Thu Mar 01 08:29:32 2018 -0500 +++ b/lib.r Wed Sep 19 03:22:21 2018 -0400 |
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| b'@@ -1,5 +1,25 @@\n # lib.r\n \n+# This function retrieve a xset like object\n+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n+getxcmsSetObject <- function(xobject) {\n+ # XCMS 1.x\n+ if (class(xobject) == "xcmsSet")\n+ return (xobject)\n+ # XCMS 3.x\n+ if (class(xobject) == "XCMSnExp") {\n+ # Get the legacy xcmsSet object\n+ suppressWarnings(xset <- as(xobject, \'xcmsSet\'))\n+ if (is.null(xset@phenoData$sample_group))\n+ sampclass(xset) = "."\n+ else\n+ sampclass(xset) <- xset@phenoData$sample_group\n+ if (!is.null(xset@phenoData$sample_name))\n+ rownames(xset@phenoData) = xset@phenoData$sample_name\n+ return (xset)\n+ }\n+}\n+\n #@author G. Le Corguille\n #The function create a pdf from the different png generated by diffreport\n diffreport_png2pdf <- function(filebase) {\n@@ -105,29 +125,29 @@\n for (n in seq(along=y)){\n if(i+n <= length(classes)){\n filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")\n- \n- diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]])\n- \n+\n+ diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]],missing=0)\n+\n diffrepOri = diffrep\n- \n+\n # renamming of the column rtmed to rt to fit with camera peaklist function output\n colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"\n colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"\n- \n+\n # combines results and reorder columns\n diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)\n diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])\n- \n+\n diffrep = RTSecondToMinute(diffrep, listArguments[["convertRTMinute"]])\n diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])\n- \n+\n if(listArguments[["sortpval"]]){\n diffrep=diffrep[order(diffrep$pvalue), ]\n }\n- \n+\n dir.create("tabular")\n write.table(diffrep, sep="\\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))\n- \n+\n if (listArguments[["eicmax"]] != 0) {\n diffreport_png2pdf(filebase)\n }\n@@ -136,7 +156,6 @@\n }\n }\n \n-\n # --- variableMetadata ---\n variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]\n variableMetadata = RTSecondToMinute(variableMetadata, listArguments[["convertRTMinute"]])\n@@ -302,3 +321,288 @@\n }\n return (directory)\n }\n+\n+#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7\n+# https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524\n+# https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd\n+############################################################\n+## getEIC\n+getEIC <- function(object, mzrange, rtrange = 200,\n+ groupidx, sampleidx = sampnames(object),\n+ rt = c("corrected", "raw'..b' xcms:::pval(testval, testclab, tstat)\n+ } else {\n+ message("Too few samples per class, skipping t-test.")\n+ tstat <- pvalue <- rep(NA,nrow(testval))\n+ }\n+ stat <- data.frame(fold = fold, tstat = tstat, pvalue = pvalue)\n+ if (length(levels(sampclass(object))) >2) {\n+ pvalAnova<-c()\n+ for(i in 1:nrow(values)){\n+ var<-as.numeric(values[i,])\n+ ano<-summary(aov(var ~ sampclass(object)) )\n+ pvalAnova<-append(pvalAnova, unlist(ano)["Pr(>F)1"])\n+ }\n+ stat<-cbind(stat, anova= pvalAnova)\n+ }\n+ if (metlin) {\n+ neutralmass <- groupmat[,"mzmed"] + ifelse(metlin < 0, 1, -1)\n+ metlin <- abs(metlin)\n+ digits <- ceiling(-log10(metlin))+1\n+ metlinurl <-\n+ paste("http://metlin.scripps.edu/simple_search_result.php?mass_min=",\n+ round(neutralmass - metlin, digits), "&mass_max=",\n+ round(neutralmass + metlin, digits), sep="")\n+ values <- cbind(metlin = metlinurl, values)\n+ }\n+ twosamp <- cbind(name = groupnames(object), stat, groupmat, values)\n+ if (sortpval) {\n+ tsidx <- order(twosamp[,"pvalue"])\n+ twosamp <- twosamp[tsidx,]\n+ rownames(twosamp) <- 1:nrow(twosamp)\n+ values<-values[tsidx,]\n+ } else\n+ tsidx <- 1:nrow(values)\n+ \n+ if (length(filebase))\n+ write.table(twosamp, paste(filebase, ".tsv", sep = ""), quote = FALSE, sep = "\\t", col.names = NA)\n+ \n+ if (eicmax > 0) {\n+ if (length(unique(peaks(object)[,"rt"])) > 1) {\n+ ## This looks like "normal" LC data\n+ \n+ eicmax <- min(eicmax, length(tsidx))\n+ eics <- getEIC(object, rtrange = eicwidth*1.1, sampleidx = ceic,\n+ groupidx = tsidx[seq(length = eicmax)])\n+ \n+ if (length(filebase)) {\n+ eicdir <- paste(filebase, "_eic", sep="")\n+ boxdir <- paste(filebase, "_box", sep="")\n+ dir.create(eicdir)\n+ dir.create(boxdir)\n+ if (capabilities("png")){\n+ xcms:::xcmsBoxPlot(values[seq(length = eicmax),],\n+ sampclass(object), dirpath=boxdir, pic="png", width=w, height=h)\n+ png(file.path(eicdir, "%003d.png"), width = w, height = h)\n+ } else {\n+ xcms:::xcmsBoxPlot(values[seq(length = eicmax),],\n+ sampclass(object), dirpath=boxdir, pic="pdf", width=w, height=h)\n+ pdf(file.path(eicdir, "%003d.pdf"), width = w/72,\n+ height = h/72, onefile = FALSE)\n+ }\n+ }\n+ plot(eics, object, rtrange = eicwidth, mzdec=mzdec)\n+ \n+ if (length(filebase))\n+ dev.off()\n+ } else {\n+ ## This looks like a direct-infusion single spectrum\n+ if (length(filebase)) {\n+ eicdir <- paste(filebase, "_eic", sep="")\n+ boxdir <- paste(filebase, "_box", sep="")\n+ dir.create(eicdir)\n+ dir.create(boxdir)\n+ if (capabilities("png")){\n+ xcmsBoxPlot(values[seq(length = eicmax),],\n+ sampclass(object), dirpath=boxdir, pic="png",\n+ width=w, height=h)\n+ png(file.path(eicdir, "%003d.png"), width = w, height = h,\n+ units = "px")\n+ } else {\n+ xcmsBoxPlot(values[seq(length = eicmax),],\n+ sampclass(object), dirpath=boxdir, pic="pdf",\n+ width=w, height=h)\n+ pdf(file.path(eicdir, "%003d.pdf"), width = w/72,\n+ height = h/72, onefile = FALSE)\n+ }\n+ }\n+ \n+ plotSpecWindow(object, gidxs = tsidx[seq(length = eicmax)], borderwidth=1)\n+ \n+ if (length(filebase))\n+ dev.off()\n+ }\n+ }\n+ \n+ invisible(twosamp)\n+}\n' |
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| diff -r 6139bfcc95cb -r a2c49996603e macros.xml --- a/macros.xml Thu Mar 01 08:29:32 2018 -0500 +++ b/macros.xml Wed Sep 19 03:22:21 2018 -0400 |
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| @@ -3,7 +3,8 @@ <xml name="requirements"> <requirements> <requirement type="package" version="0.4_2">r-snow</requirement> - <requirement type="package" version="1.32.0">bioconductor-camera</requirement> + <requirement type="package" version="3.0.0">bioconductor-xcms</requirement> + <requirement type="package" version="1.34.0">bioconductor-camera</requirement> <requirement type="package" version="2.28.0">bioconductor-multtest</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> <requirement type="package" version="1.3.23">graphicsmagick</requirement> |
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| diff -r 6139bfcc95cb -r a2c49996603e repository_dependencies.xml --- a/repository_dependencies.xml Thu Mar 01 08:29:32 2018 -0500 +++ b/repository_dependencies.xml Wed Sep 19 03:22:21 2018 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories> <repository changeset_revision="4a51ab3d8ecf" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r 6139bfcc95cb -r a2c49996603e test-data/.RData |
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| Binary file test-data/.RData has changed |
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| diff -r 6139bfcc95cb -r a2c49996603e test-data/CMD.mac.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CMD.mac.sh Wed Sep 19 03:22:21 2018 -0400 |
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| @@ -0,0 +1,1 @@ +LC_ALL=C Rscript ../CAMERA.r xfunction annotatediff image 'faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData' nSlaves ${GALAXY_SLOTS:-1} variableMetadataOutput variableMetadataOutput.txt dataMatrixOutput dataMatrixOutput.txt sigma 6 perfwhm 0.6 ppm 5 mzabs 0.015 maxcharge 3 maxiso 4 minfrac 0.5 quick TRUE xsetRdataOutput '/tmp/tmpT41cRC/files/000/dataset_20.dat' runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 convertRTMinute TRUE numDigitsMZ 4 numDigitsRT 1 intval into singlefile_galaxyPath 'wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF' singlefile_sampleName 'wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF' |
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| diff -r 6139bfcc95cb -r a2c49996603e test-data/Rplots.pdf |
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| Binary file test-data/Rplots.pdf has changed |
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| diff -r 6139bfcc95cb -r a2c49996603e test-data/dataMatrixOutput.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataMatrixOutput.txt Wed Sep 19 03:22:21 2018 -0400 |
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| b'@@ -0,0 +1,6333 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|
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| diff -r 6139bfcc95cb -r a2c49996603e test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData |
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| Binary file test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData has changed |
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| diff -r 6139bfcc95cb -r a2c49996603e test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix-xcms3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix-xcms3.tsv Wed Sep 19 03:22:21 2018 -0400 |
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|
| b |
| diff -r 6139bfcc95cb -r a2c49996603e test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv Wed Sep 19 03:22:21 2018 -0400 |
| b |
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|