| Previous changeset 18:cb923396e70f (2019-08-29) Next changeset 20:b979ba5888f7 (2020-03-18) |
|
Commit message:
"planemo upload commit 4fcbbcbc6d6b0a59e801870d31fe886a920ef429" |
|
modified:
CAMERA_annotateDiffreport.r README.rst abims_CAMERA_annotateDiffreport.xml lib.r macros.xml |
| b |
| diff -r cb923396e70f -r 01459b73daf9 CAMERA_annotateDiffreport.r --- a/CAMERA_annotateDiffreport.r Thu Aug 29 11:38:21 2019 -0400 +++ b/CAMERA_annotateDiffreport.r Thu Feb 13 17:23:07 2020 -0500 |
| b |
| @@ -45,6 +45,7 @@ args = rawFilePath$args directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) + # Because so far CAMERA isn't compatible with the new XCMSnExp object if (exists("xdata")){ xset <- getxcmsSetObject(xdata) |
| b |
| diff -r cb923396e70f -r 01459b73daf9 README.rst --- a/README.rst Thu Aug 29 11:38:21 2019 -0400 +++ b/README.rst Thu Feb 13 17:23:07 2020 -0500 |
| b |
| @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 2.2.5+camera1.42.0 - 13/02/2020** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 1.42.0 (see CAMERA News_) + **Version 2.2.5 - 09/04/2019** - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables |
| b |
| diff -r cb923396e70f -r 01459b73daf9 abims_CAMERA_annotateDiffreport.xml --- a/abims_CAMERA_annotateDiffreport.xml Thu Aug 29 11:38:21 2019 -0400 +++ b/abims_CAMERA_annotateDiffreport.xml Thu Feb 13 17:23:07 2020 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5+camera@TOOL_VERSION@+galaxy0"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> @@ -436,6 +436,8 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS +@HELP_CAMERA_NEWVERSION_1420@ + **Version 2.2.5 - 09/04/2019** - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables |
| b |
| diff -r cb923396e70f -r 01459b73daf9 lib.r --- a/lib.r Thu Aug 29 11:38:21 2019 -0400 +++ b/lib.r Thu Feb 13 17:23:07 2020 -0500 |
| [ |
| b'@@ -366,287 +366,3 @@\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")) {\n-\n- files <- filepaths(object)\n- grp <- groups(object)\n- samp <- sampnames(object)\n- prof <- profinfo(object)\n-\n- rt <- match.arg(rt)\n-\n- if (is.numeric(sampleidx))\n- sampleidx <- sampnames(object)[sampleidx]\n- sampidx <- match(sampleidx, sampnames(object))\n-\n- if (!missing(groupidx)) {\n- if (is.numeric(groupidx))\n- groupidx <- groupnames(object)[unique(as.integer(groupidx))]\n- grpidx <- match(groupidx, groupnames(object, template = groupidx))\n- }\n-\n- if (missing(mzrange)) {\n- if (missing(groupidx))\n- stop("No m/z range or groups specified")\n- if (any(is.na(groupval(object, value = "mz"))))\n- warning(\n- "`NA` values in xcmsSet. Use fillPeaks() on the object to fill",\n- "-in missing peak values. Note however that this will also ",\n- "insert intensities of 0 for peaks that can not be filled in.")\n- mzmin <- apply(groupval(object, value = "mzmin"), 1, min, na.rm = TRUE)\n- mzmax <- apply(groupval(object, value = "mzmax"), 1, max, na.rm = TRUE)\n- mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)\n- ## if (any(is.na(groupval(object, value = "mz"))))\n- ## stop(\'Please use fillPeaks() to fill up NA values !\')\n- ## mzmin <- -rowMax(-groupval(object, value = "mzmin"))\n- ## mzmax <- rowMax(groupval(object, value = "mzmax"))\n- ## mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)\n- } else if (all(c("mzmin","mzmax") %in% colnames(mzrange)))\n- mzrange <- mzrange[,c("mzmin", "mzmax"),drop=FALSE]\n- else if (is.null(dim(mzrange)))\n- stop("mzrange must be a matrix")\n- colnames(mzrange) <- c("mzmin", "mzmax")\n-\n- if (length(rtrange) == 1) {\n- if (missing(groupidx))\n- rtrange <- matrix(rep(range(object@rt[[rt]][sampidx]), nrow(mzrange)),\n- ncol = 2, byrow = TRUE)\n- else {\n- rtrange <- retexp(grp[grpidx,c("rtmin","rtmax"),drop=FALSE], rtrange)\n- }\n- } else if (is.null(dim(rtrange)))\n- stop("rtrange must be a matrix or single number")\n- colnames(rtrange) <- c("rtmin", "rtmax")\n-\n- ## Ensure that we\'ve got corrected retention time if requested.\n- if (is.null(object@rt[[rt]]))\n- stop(rt, " retention times not present in \'object\'!")\n-\n- ## Ensure that the defined retention time range is within the rtrange of the\n- ## object: we\'re using the max minimal rt of all files and the min maximal rt\n- rtrs <- lapply(object@rt[[rt]], range)\n- rtr <- c(max(unlist(lapply(rtrs, "[", 1))),\n- min(unlist(lapply(rtrs, "[", 2))))\n- ## Check if we\'ve got a range which is completely off:\n- if (any(rtrange[, "rtmin"] >= rtr[2] | rtrange[, "rtmax"] <= rtr[1])) {\n- outs <- which(rtrange[, "rtmin"] >= rtr[2] |\n- rtrange[, "rtmax"] <= rtr[1])\n- stop(length(outs), " of the specified \'rtrange\' are completely outside ",\n- "of the retention time range of \'object\' which is (", rtr[1], ", ",\n- rtr[2], "). The first was: (", rtrange[outs[1], "rtmin"], ", ",\n- rtrange[outs[1], "rtmax"], "!")\n- }\n- lower_rt_outside <- rtrange[, "rtmin"] < rtr[1]\n- upper_rt_outside <- rtrange[, "rtmax"] > rtr[2]\n- if (any(lower_rt_outside) | any(upper_rt_outside)) {\n- ## Silently fix these ranges.\n- rtrange[lower_rt_outside, "rtmin"] <- rtr[1]\n- rtrange[upper_rt_outside, "rtmax"] <- rtr[2]\n- }\n-\n- if (missing(groupidx))\n- '..b'- tstat <- mt.teststat(testval, testclab, ...)\n- pvalue <- 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' |
| b |
| diff -r cb923396e70f -r 01459b73daf9 macros.xml --- a/macros.xml Thu Aug 29 11:38:21 2019 -0400 +++ b/macros.xml Thu Feb 13 17:23:07 2020 -0500 |
| b |
| @@ -1,11 +1,13 @@ <?xml version="1.0"?> <macros> + + <token name="@TOOL_VERSION@">1.42.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="0.4_3">r-snow</requirement> - <requirement type="package" version="1.38.1">bioconductor-camera</requirement> - <requirement type="package" version="2.38.0">bioconductor-multtest</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-camera</requirement> + <requirement type="package" version="2.42.0">bioconductor-multtest</requirement> + <requirement type="package" version="1.1_5">r-batch</requirement> <requirement type="package" version="1.3.31">graphicsmagick</requirement> </requirements> </xml> @@ -158,6 +160,11 @@ </token> + <token name="@HELP_CAMERA_NEWVERSION_1420@"> +**Version 2.2.5+camera1.42.0 - 13/02/2020** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 1.42.0 (see CAMERA News_) + </token> <xml name="citation"> <citations> |