| Previous changeset 8:8c5bb7b86df9 (2016-02-22) Next changeset 10:8dd6f0ffa763 (2016-07-04) |
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Commit message:
planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b |
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modified:
README.rst abims_CAMERA_annotateDiffreport.xml tool_dependencies.xml |
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added:
CAMERA.r lib.r macros.xml planemo_test.sh test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv test-data/faahKO.xset.group.retcor.group.fillpeaks.RData test-data/faahKO_reduce.zip |
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removed:
Makefile planemo.sh test-data/xset.group.retcor.group.fillPeaks.RData test-data/xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv test-data/xset.group.retcor.group.fillPeaks.annotate.negative.Rdata test-data/xset.group.retcor.group.fillPeaks.annotate.variableMetadata.Xdiffreport.zip test-data/xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv |
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| diff -r 8c5bb7b86df9 -r 7da9252dd983 CAMERA.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CAMERA.r Mon Apr 25 11:06:25 2016 -0400 |
| [ |
| @@ -0,0 +1,175 @@ +#!/usr/bin/env Rscript +# CAMERA.r version="2.2.1" + + + +# ----- PACKAGE ----- +cat("\tPACKAGE INFO\n") + +setRepositories(graphics=F, ind=31) + +#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="") +} +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"); + + + +# ----- 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') + +cat("\n\n"); + + +# ----- PROCESSING INFILE ----- +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 +} + +if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) { + load(listArguments[["image_pos"]]) + xaP=xa + listOFlistArgumentsP=listOFlistArguments + if (exists("xsAnnotate_object")) xaP=xsAnnotate_object + + diffrepP=NULL + if (exists("diffrep")) diffrepP=diffrep + + load(listArguments[["image_neg"]]) + xaN=xa + listOFlistArgumentsN=listOFlistArguments + if (exists("xsAnnotate_object")) xaN=xsAnnotate_object + + diffrepN=NULL + if (exists("diffrep")) diffrepN=diffrep +} + + +cat("\n\n") + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tARGUMENTS PROCESSING INFO\n") + +# Save arguments to generate a report +if (!exists("listOFlistArguments")) listOFlistArguments=list() +listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments + + +#saving the commun parameters +thefunction = listArguments[["xfunction"]] +listArguments[["xfunction"]]=NULL #delete from the list of arguments + +xsetRdataOutput = paste(thefunction,"RData",sep=".") +if (!is.null(listArguments[["xsetRdataOutput"]])){ + xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL +} + +rplotspdf = "Rplots.pdf" +if (!is.null(listArguments[["rplotspdf"]])){ + rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL +} + +dataMatrixOutput = "dataMatrix.tsv" +if (!is.null(listArguments[["dataMatrixOutput"]])){ + dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL +} + +variableMetadataOutput = "variableMetadata.tsv" +if (!is.null(listArguments[["variableMetadataOutput"]])){ + variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL +} + +if (!is.null(listArguments[["new_file_path"]])){ + new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL +} + +#Import the different functions +source_local("lib.r") + +#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 +} + +# We unzip automatically the chromatograms from the zip files. +if (thefunction %in% c("annotatediff")) { + 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) + } + + #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 xset object to the list of arguments in the first position +if (exists("xset") != 0){ + listArguments=append(list(xset), listArguments) +} + +cat("\n\n") + + + + +# ----- PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + +#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,new_file_path=new_file_path) + xa=results_list[["xa"]] + diffrep=results_list[["diffrep"]] + variableMetadata=results_list[["variableMetadata"]] + + cat("\n\n") + cat("\tXSET OBJECT INFO\n") + print(xa) +} + +if (thefunction %in% c("combinexsAnnos")) { + cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput) +} + +dev.off() + + +#saving R data in .Rdata file to save the variables used in the present tool +objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile") +save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) + +cat("\n\n") + +cat("\tDONE\n") |
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| diff -r 8c5bb7b86df9 -r 7da9252dd983 Makefile --- a/Makefile Mon Feb 22 16:48:11 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,23 +0,0 @@ -# USAGE: make [install|clean] - -# -------- VARIABLE -------- - -OBJ=camera_annotate.tgz -DEP=abims_CAMERA_annotateDiffreport.xml tool_dependencies.xml repository_dependencies.xml static test-data - - -# ------------------------ - -all: $(OBJ) - -$(OBJ): $(DEP) - tar --exclude=".svn" -zchf $@ $^ - -# ------------------------ - -install: $(OBJ) - mv *.tgz ~ - -clean: - rm *.tgz - |
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| diff -r 8c5bb7b86df9 -r 7da9252dd983 README.rst --- a/README.rst Mon Feb 22 16:48:11 2016 -0500 +++ b/README.rst Mon Apr 25 11:06:25 2016 -0400 |
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| @@ -2,7 +2,16 @@ Changelog/News -------------- -**Version 2.1.3 - 10/02/2016** +**Version 2.1.5 - 21/04/2016** + +- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 + + +**Version 2.1.4 - 18/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + +**Version 2.1.3 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed @@ -27,3 +36,12 @@ - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions + +Test Status +----------- + +Planemo test using conda: passed + +Planemo test using source env.sh: passed + +Planemo shed_test : passed |
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| diff -r 8c5bb7b86df9 -r 7da9252dd983 abims_CAMERA_annotateDiffreport.xml --- a/abims_CAMERA_annotateDiffreport.xml Mon Feb 22 16:48:11 2016 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Mon Apr 25 11:06:25 2016 -0400 |
| [ |
| b'@@ -1,24 +1,16 @@\n-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3">\n+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5">\n \n <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>\n \n- <requirements>\n- <requirement type="package" version="3.1.2">R</requirement>\n- <requirement type="binary">Rscript</requirement>\n- <requirement type="package" version="1.44.0">xcms</requirement>\n- <requirement type="package" version="1.22.0">camera</requirement>\n- <requirement type="package" version="2.2.1">camera_w4m_script</requirement>\n- <requirement type="binary">CAMERA.r</requirement>\n- <requirement type="package" version="1.3.18">graphicsmagick</requirement>\n- <requirement type="binary">convert</requirement>\n- </requirements>\n- \n- <stdio>\n- <exit_code range="1:" level="fatal" />\n- </stdio>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n \n <command><![CDATA[\n- CAMERA.r \n+ @COMMAND_CAMERA_SCRIPT@\n xfunction annotatediff \n image $image\n \n@@ -56,7 +48,10 @@\n new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_\n #end if\n \n- \n+ #if $zip_file:\n+ zipfile $zip_file\n+ #end if\n+\n ]]></command>\n \n <inputs>\n@@ -131,7 +126,9 @@\n <when value="hide">\n </when>\n </conditional>\n- \n+\n+ <!-- To pass planemo test -->\n+ <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />\n </inputs>\n \n <outputs>\n@@ -143,13 +140,13 @@\n <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />\n </change_format>\n </data>\n-\t<data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">\n-\t\t <filter>(options[\'option\'] == \'show\')</filter>\n-\t</data> \n+ <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">\n+\t\t <filter>(options[\'option\'] == \'show\')</filter>\n+\t </data> \n </outputs>\n \n <tests>\n- <test>\n+ <!--<test>\n <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/>\n <param name="convert_param" value="False"/>\n <param name="num_digits" value="0"/>\n@@ -162,26 +159,60 @@\n <param name="mzabs" value="0.015"/>\n <param name="intval" value="into"/>\n <param name="max_peaks" value="100"/>\n- <param name="quick_block.quick" value="FALSE"/>\n- <param name="quick_block.polarity" value="negative"/>\n- <param name="quick_block.cor_eic_th" value="0.75"/>\n- <param name="quick_block.graphMethod" value="hcs"/>\n- <param name="quick_block.pval" value="0.05"/>\n- <param name="quick_block.calcCiS" value="True"/>\n- <param name="quick_block.calcIso" value="False"/>\n- <param name="quick_block.calcCaS" value="False"/>\n- <param name="quick_block.multiplier" value="3"/>\n- <param name="options.option" value="show"/>\n- <param name="options.eicmax" value="200"/>\n- <param name="options.eicwidth" value="200"/>\n- <param name="options.value" value="into"/>\n- <param name="options.h" value="480"/>\n- <param name="options.w" value="640"/>\n- <param name="options.mzdec" value="2"/>\n- <param name="options.sortpval" value="False"/>\n+ <param name="quick_block|quick" value="FALSE"/>\n+ <param name'..b' <param name="options|value" value="into"/>\n+ <param name="options|h" value="480"/>\n+ <param name="options|w" value="640"/>\n+ <param name="options|mzdec" value="2"/>\n+ <param name="options|sortpval" value="False"/>\n+ <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />\n <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />\n <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />\n- <output name="rdata" file="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />\n+ </test>-->\n+ <test>\n+ <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/>\n+ <param name="convert_param" value="False"/>\n+ <param name="num_digits" value="0"/>\n+ <param name="sigma" value="6"/>\n+ <param name="perfwhm" value="0.6"/>\n+ <param name="maxcharge" value="3"/>\n+ <param name="maxiso" value="4"/>\n+ <param name="minfrac" value="0.5"/>\n+ <param name="ppm" value="5"/>\n+ <param name="mzabs" value="0.015"/>\n+ <param name="intval" value="into"/>\n+ <param name="max_peaks" value="100"/>\n+ <param name="quick_block|quick" value="FALSE"/>\n+ <param name="quick_block|polarity" value="negative"/>\n+ <param name="quick_block|cor_eic_th" value="0.75"/>\n+ <param name="quick_block|graphMethod" value="hcs"/>\n+ <param name="quick_block|pval" value="0.05"/>\n+ <param name="quick_block|calcCiS" value="True"/>\n+ <param name="quick_block|calcIso" value="False"/>\n+ <param name="quick_block|calcCaS" value="False"/>\n+ <param name="quick_block|multiplier" value="3"/>\n+ <param name="options|option" value="show"/>\n+ <param name="options|eicmax" value="200"/>\n+ <param name="options|eicwidth" value="200"/>\n+ <param name="options|value" value="into"/>\n+ <param name="options|h" value="480"/>\n+ <param name="options|w" value="640"/>\n+ <param name="options|mzdec" value="2"/>\n+ <param name="options|sortpval" value="False"/>\n+ <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" />\n+ <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />\n+ <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />\n </test>\n </tests>\n \n@@ -189,18 +220,7 @@\n \n <help><![CDATA[\n \n-.. class:: infomark\n-\n-**Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de\n-\n-.. class:: infomark\n-\n-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]\n-\n- | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.\n-\n----------------------------------------------------\n-\n+@HELP_AUTHORS@\n \n ================\n CAMERA.annotate\n@@ -378,7 +398,17 @@\n Changelog/News\n --------------\n \n-**Version 2.1.3 - 10/02/2016**\n+**Version 2.1.5 - 21/04/2016**\n+\n+- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0\n+\n+\n+**Version 2.1.4 - 18/04/2016**\n+\n+- TEST: refactoring to pass planemo test using conda dependencies\n+\n+\n+**Version 2.1.3 - 10/02/2016**\n \n - BUGFIX: better management of errors. Datasets remained green although the process failed\n \n@@ -405,10 +435,7 @@\n \n ]]></help>\n \n- <citations>\n- <citation type="doi">10.1021/ac202450g</citation>\n- <citation type="doi">10.1093/bioinformatics/btu813</citation>\n- </citations>\n+ <expand macro="citation" />\n \n \n </tool>\n' |
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| diff -r 8c5bb7b86df9 -r 7da9252dd983 lib.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Mon Apr 25 11:06:25 2016 -0400 |
| [ |
| b'@@ -0,0 +1,188 @@\n+# lib.r version="2.2.1"\n+\n+#The function create a pdf from the different png generated by diffreport\n+diffreport_png2pdf <- function(filebase, new_file_path) {\n+\n+ pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="")\n+ pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="")\n+\n+ system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep=""))\n+ system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep=""))\n+\n+ file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput)\n+ file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput)\n+}\n+\n+#The function annotateDiffreport without the corr function which bugs\n+annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) {\n+ # Resolve the bug with x11, with the function png\n+ options(bitmapType=\'cairo\')\n+\n+ #Check if the fillpeaks step has been done previously, if it hasn\'t, there is an error message and the execution is stopped.\n+ res=try(is.null(xset@filled))\n+\n+ # ------ annot -------\n+ listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])\n+ listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])\n+ listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])\n+\n+ #graphMethod parameter bugs where this parameter is not defined in quick=true\n+ if(listArguments[["quick"]]==TRUE) {\n+ xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])\n+ }\n+ else {\n+ xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]],multiplier=listArguments[["multiplier"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])\n+\n+ } \n+ peakList=getPeaklist(xa,intval=listArguments[["intval"]])\n+ peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");\n+\n+\n+ # --- Multi condition : diffreport --- \n+ diffrep=NULL\n+ if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {\n+ #Check if the fillpeaks step has been done previously, if it hasn\'t, there is an error message and the execution is stopped.\n+ res=try(is.null(xset@filled))\n+ classes=levels(sampclass(xset))\n+ x=1:(length(classes)-1)\n+ for (i in seq(along=x) ) {\n+ y=1:(length(classes))\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+ #combines results\n+ diffreportTSV=merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)\n+ diffreportTSV=cbind(diffreportTSV[,!(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))],diffreportTSV[,(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))])\n+\n+ if(listArguments[["sortpval"]]){\n+ diffreportTSV=diffr'..b'["num_digits"]]),"T",round(variableMetadata$rt),sep="") \n+ write.table(variableMetadata, sep="\\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)\n+\n+ # --- dataMatrix ---\n+ dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]\n+ dataMatrix=cbind(peakList$name,dataMatrix); colnames(dataMatrix)[1] = c("name");\n+\n+ if (listArguments[["convert_param"]]){\n+ #converting the retention times (seconds) into minutes\n+ print("converting the retention times into minutes in the dataMatrix ids")\n+ peakList$rt=peakList$rt/60\n+ }\n+ dataMatrix$name= paste("M",round(peakList$mz,digits=listArguments[["num_digits"]]),"T",round(peakList$rt),sep="")\n+ write.table(dataMatrix, sep="\\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)\n+ \n+ return(list("xa"=xa,"diffrep"=diffrep,"variableMetadata"=variableMetadataOri));\n+\n+}\n+\n+\n+combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){\n+\n+ #Load the two Rdata to extract the xset objects from positive and negative mode\n+ cat("\\tObject xset from positive mode\\n")\n+ print(xaP)\n+ cat("\\n") \n+\n+ cat("\\tObject xset from negative mode\\n")\n+ print(xaN)\n+ cat("\\n")\n+ \n+ cat("\\n")\n+ cat("\\tCombining...\\n")\n+ #Convert the string to numeric for creating matrix\n+ row=as.numeric(strsplit(ruleset,",")[[1]][1])\n+ column=as.numeric(strsplit(ruleset,",")[[1]][2])\n+ ruleset=cbind(row,column)\n+ #Test if the file comes from an older version tool\n+ if ((!is.null(xaP)) & (!is.null(xaN))) {\n+ #Launch the combinexsannos function from CAMERA\n+ cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)\n+ } else {\n+ stop("You must relauch the CAMERA.annotate step with the lastest version.")\n+ }\n+\n+ \n+\n+ if(pos){\n+ xa=xaP\n+ listOFlistArgumentsP=listOFlistArguments\n+ mode="neg. Mode"\n+ } else {\n+ xa=xaN\n+ listOFlistArgumentsN=listOFlistArguments\n+ mode="pos. Mode"\n+ }\n+ intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval }\n+ peakList=getPeaklist(xa,intval=intval)\n+ peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");\n+ variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);\n+ variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]\n+\n+ #Test if there are more than two classes (conditions)\n+ if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {\n+ diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")\n+ diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")\n+ \n+ variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")\n+ variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")\n+ } \n+ \n+ rownames(variableMetadata) = NULL\n+ #TODO: checker\n+ #colnames(variableMetadata)[1:2] = c("name","mz/rt");\n+\n+ #If the user want to convert the retention times (seconds) into minutes.\n+ if (listArguments[["convert_param"]]){\n+ #converting the retention times (seconds) into minutes\n+ cat("\\tConverting the retention times into minutes\\n")\n+ variableMetadata$rtmed=cAnnot$rt/60; variableMetadata$rtmin=cAnnot$rtmin/60; variableMetadata$rtmax=cAnnot$rtmax/60;\n+ }\n+\n+ #If the user want to keep only the metabolites which match a difference\n+ if(keep_meta){\n+ variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]\n+ }\n+ \n+ #Write the output into a tsv file\n+ write.table(variableMetadata, sep="\\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)\n+ return(variableMetadata);\n+\n+}\n' |
| b |
| diff -r 8c5bb7b86df9 -r 7da9252dd983 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Apr 25 11:06:25 2016 -0400 |
| [ |
| @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.26.0">bioconductor-camera</requirement> + <requirement type="package" version="2.26.0">bioconductor-multtest</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.6.17">libpng</requirement> + <requirement type="package" version="1.3.20">graphicsmagick</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + </xml> + + <token name="@COMMAND_CAMERA_SCRIPT@"> + LANG=C Rscript $__tool_directory__/CAMERA.r + </token> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +--------------------------------------------------- + + </token> + + + <xml name="citation"> + <citations> + <citation type="doi">10.1021/ac202450g</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 8c5bb7b86df9 -r 7da9252dd983 planemo.sh --- a/planemo.sh Mon Feb 22 16:48:11 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -planemo shed_init -f --name=camera_annotate --owner=lecorguille --description="[W4M][GC-MS] CAMERA R Package - Preprocessing - Returns annotation results (isotope peaks, adducts and fragments)" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html Wrapper skript for automatic annotation of isotope peaks, adducts and fragments for a (grouped) xcmsSet xs. The function returns an xsAnnotate object. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too" --category="Metabolomics" |
| b |
| diff -r 8c5bb7b86df9 -r 7da9252dd983 planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Mon Apr 25 11:06:25 2016 -0400 |
| [ |
| @@ -0,0 +1,29 @@ +# Example of planemo command to launch test + +# Note: --galaxy_branch "dev" is set to deal with zip file + + +# -- Use of installed package environments +# after having installing package on a local galaxy instance +source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh +source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh +planemo test --install_galaxy --galaxy_branch "dev" + +#All 1 test(s) executed passed. +#abims_CAMERA_annotateDiffreport[0]: passed + + +# -- 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 --galaxy_branch "dev" + +#All 1 test(s) executed passed. +#abims_CAMERA_annotateDiffreport[0]: passed + + +# -- Use of shed_test +planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch "dev" + +#All 1 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: passed |
| b |
| diff -r 8c5bb7b86df9 -r 7da9252dd983 test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv Mon Apr 25 11:06:25 2016 -0400 |
| b |
| b'@@ -0,0 +1,8158 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|
| b |
| diff -r 8c5bb7b86df9 -r 7da9252dd983 test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Mon Apr 25 11:06:25 2016 -0400 |
| [ |
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| diff -r 8c5bb7b86df9 -r 7da9252dd983 test-data/xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv --- a/test-data/xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv Mon Feb 22 16:48:11 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 8c5bb7b86df9 -r 7da9252dd983 test-data/xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv --- a/test-data/xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv Mon Feb 22 16:48:11 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,10502 +0,0 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|
| b |
| diff -r 8c5bb7b86df9 -r 7da9252dd983 tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 22 16:48:11 2016 -0500 +++ b/tool_dependencies.xml Mon Apr 25 11:06:25 2016 -0400 |
| b |
| @@ -1,15 +1,12 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.1.2"> - <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="camera" version="1.22.0"> - <repository changeset_revision="845eb883bd1b" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="camera_w4m_script" version="2.2.1"> - <repository changeset_revision="91b0d23c9d52" name="package_camera_w4m_script_2_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="bioconductor-camera" version="1.26.0"> + <repository changeset_revision="fd308c76626b" name="package_bioconductor_camera_1_26_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="graphicsmagick" version="1.3.18"> - <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="graphicsmagick" version="1.3.20"> + <repository changeset_revision="f2855f4cbc8f" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |