| Previous changeset 17:73d82de36369 (2018-10-09) Next changeset 19:01459b73daf9 (2020-02-13) |
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Commit message:
planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c |
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modified:
README.rst abims_CAMERA_annotateDiffreport.xml lib.r macros.xml repository_dependencies.xml |
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added:
CAMERA_annotateDiffreport.r |
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removed:
CAMERA.r planemo_test.sh test-data/.RData test-data/CMD.mac.sh test-data/Rplots.pdf test-data/dataMatrixOutput.txt |
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| diff -r 73d82de36369 -r cb923396e70f CAMERA.r --- a/CAMERA.r Tue Oct 09 06:03:01 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,157 +0,0 @@ -#!/usr/bin/env Rscript -# CAMERA.r version="2.2.1" - - - -# ----- PACKAGE ----- -cat("\tSESSION INFO\n") - -pkgs=c("CAMERA","multtest","batch") -for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) - -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"); - - - -# ----- 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 -} - -variableMetadataOutput = "variableMetadata.tsv" -if (!is.null(listArguments[["variableMetadataOutput"]])){ - variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL -} - -#Import the different functions -source_local("lib.r") - -# We unzip automatically the chromatograms from the zip files. -if (thefunction %in% c("annotatediff")) { - if (!exists("zipfile")) zipfile=NULL - if (!exists("singlefile")) singlefile=NULL - rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) - zipfile = rawFilePath$zipfile - singlefile = rawFilePath$singlefile - listArguments = rawFilePath$listArguments - 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")){ - 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) - 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, - pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]], - convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]], - 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","singlefile") -save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) - -cat("\n\n") - -cat("\tDONE\n") |
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| diff -r 73d82de36369 -r cb923396e70f CAMERA_annotateDiffreport.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CAMERA_annotateDiffreport.r Thu Aug 29 11:38:21 2019 -0400 |
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| @@ -0,0 +1,78 @@ +#!/usr/bin/env Rscript + +# ----- PACKAGE ----- +cat("\tSESSION INFO\n") + +#Import the different functions +source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +source_local("lib.r") + +pkgs=c("CAMERA","multtest","batch") +loadAndDisplayPackages(pkgs) +cat("\n\n"); + +# ----- ARGUMENTS ----- +cat("\tARGUMENTS INFO\n") + +args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(args), 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 +load(args$image); args$image=NULL + +cat("\n\n") + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tARGUMENTS PROCESSING INFO\n") + +# Save arguments to generate a report +if (!exists("listOFargs")) listOFargs=list() +listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] = args + +# We unzip automatically the chromatograms from the zip files. +if (!exists("zipfile")) zipfile=NULL +if (!exists("singlefile")) singlefile=NULL +rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, args) +zipfile = rawFilePath$zipfile +singlefile = rawFilePath$singlefile +args = rawFilePath$args +directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) + +# Because so far CAMERA isn't compatible with the new XCMSnExp object +if (exists("xdata")){ + xset <- getxcmsSetObject(xdata) +} + +cat("\n\n") + + +# ----- PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + +results_list=annotatediff(xset=xset,args=args,variableMetadataOutput="variableMetadata.tsv") +xa=results_list$xa +diffrep=results_list$diffrep +variableMetadata=results_list$variableMetadata + +cat("\n\n") + +# ----- EXPORT ----- + +cat("\tXSET OBJECT INFO\n") +print(xa) +cat("\n\n") + +#saving R data in .Rdata file to save the variables used in the present tool +objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile") +save(list=objects2save[objects2save %in% ls()], file="annotatediff.RData") + +cat("\n\n") + +cat("\tDONE\n") |
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| diff -r 73d82de36369 -r cb923396e70f README.rst --- a/README.rst Tue Oct 09 06:03:01 2018 -0400 +++ b/README.rst Thu Aug 29 11:38:21 2019 -0400 |
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| @@ -2,6 +2,14 @@ Changelog/News -------------- +**Version 2.2.5 - 09/04/2019** + +- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + +- UPGRADE: refactoring of internal code + **Version 2.2.4 - 09/10/2018** - NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job |
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| diff -r 73d82de36369 -r cb923396e70f abims_CAMERA_annotateDiffreport.xml --- a/abims_CAMERA_annotateDiffreport.xml Tue Oct 09 06:03:01 2018 -0400 +++ b/abims_CAMERA_annotateDiffreport.xml Thu Aug 29 11:38:21 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.4"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> @@ -10,15 +10,11 @@ <expand macro="stdio"/> <command><![CDATA[ - @COMMAND_CAMERA_SCRIPT@ - xfunction annotatediff + @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r image '$image' nSlaves \${GALAXY_SLOTS:-1} - ## output - variableMetadataOutput '$variableMetadata' - ## groupFWHM sigma $groupfwhm.sigma perfwhm $groupfwhm.perfwhm @@ -34,8 +30,6 @@ quick $quick_block.quick #if $quick_block.quick == "FALSE": - xsetRdataOutput '$rdata_quick_false' - ## groupcorr cor_eic_th $quick_block.groupcorr.cor_eic_th graphMethod $quick_block.groupcorr.graphMethod @@ -52,8 +46,6 @@ #else rules $quick_block.findadducts.rules_block.rules #end if - #else - xsetRdataOutput '$rdata_quick_true' #end if #if $diffreport.options.option == "show": @@ -66,6 +58,8 @@ h $diffreport.options.h w $diffreport.options.w mzdec $diffreport.options.mzdec + tabular2 $diffreport.options.tabular2 + png2 $diffreport.options.png2 #end if @COMMAND_PEAKLIST@ @@ -159,6 +153,14 @@ <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> + <param name="tabular2" type="select" label="Export the Diffreport files in "> + <option value="zip" selected="true">Zip</option> + <option value="datasetcollection">Individual file in a Dataset Collection</option> + </param> + <param name="png2" type="select" label="Export the EIC and boxplots in "> + <option value="zip" selected="true">Zip</option> + <option value="pdf">Individual pdf</option> + </param> </when> <when value="hide"> </when> @@ -170,22 +172,36 @@ </inputs> <outputs> - <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> - <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" > + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" /> + <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" from_work_dir="annotatediff.RData"> <filter>quick_block['quick'] == 'FALSE'</filter> <change_format> <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" /> <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" /> </change_format> </data> - <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" > + <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" from_work_dir="annotatediff.RData"> <filter>quick_block['quick'] == 'TRUE'</filter> </data> - <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true"> - <filter>diffreport['options']['option'] == 'show'</filter> - <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" /> - <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" /> + + <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" > + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter> + </data> + <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" > + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter> </data> + <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf"> + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter> + <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" /> + </collection> + + <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.zip" from_work_dir="tabular.zip"> + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter> + </data> + <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table"> + <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter> + <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" /> + </collection> </outputs> <tests> @@ -418,9 +434,19 @@ Changelog/News -------------- +.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS + +**Version 2.2.5 - 09/04/2019** + +- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + +- UPGRADE: refactoring of internal code + **Version 2.2.4 - 09/10/2018** -- NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job +- NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job **Version 2.2.3 - 30/04/2018** |
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| diff -r 73d82de36369 -r cb923396e70f lib.r --- a/lib.r Tue Oct 09 06:03:01 2018 -0400 +++ b/lib.r Thu Aug 29 11:38:21 2019 -0400 |
| [ |
| b'@@ -1,5 +1,31 @@\n # lib.r\n \n+#@author G. Le Corguille\n+# solve an issue with batch if arguments are logical TRUE/FALSE\n+parseCommandArgs <- function(...) {\n+ args <- batch::parseCommandArgs(...)\n+ for (key in names(args)) {\n+ if (args[key] %in% c("TRUE","FALSE"))\n+ args[key] = as.logical(args[key])\n+ }\n+ return(args)\n+}\n+\n+#@author G. Le Corguille\n+# This function will\n+# - load the packages\n+# - display the sessionInfo\n+loadAndDisplayPackages <- function(pkgs) {\n+ for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))\n+\n+ sessioninfo = sessionInfo()\n+ cat(sessioninfo$R.version$version.string,"\\n")\n+ cat("Main packages:\\n")\n+ for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\\t") }; cat("\\n")\n+ cat("Other loaded packages:\\n")\n+ for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\\t") }; cat("\\n")\n+}\n+\n # This function retrieve a xset like object\n #@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n getxcmsSetObject <- function(xobject) {\n@@ -34,6 +60,18 @@\n }\n \n #@author G. Le Corguille\n+#The function create a zip archive from the different png generated by diffreport\n+diffreport_png2zip <- function() {\n+ zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip"))\n+ zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip"))\n+}\n+\n+#The function create a zip archive from the different tabular generated by diffreport\n+diffreport_tabular2zip <- function() {\n+ zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip"))\n+}\n+\n+#@author G. Le Corguille\n #This function convert if it is required the Retention Time in minutes\n RTSecondToMinute <- function(variableMetadata, convertRTMinute) {\n if (convertRTMinute){\n@@ -57,7 +95,7 @@\n }\n \n #The function annotateDiffreport without the corr function which bugs\n-annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv") {\n+annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") {\n # Resolve the bug with x11, with the function png\n options(bitmapType=\'cairo\')\n \n@@ -65,52 +103,52 @@\n res=try(is.null(xset@filled))\n \n # ------ annot -------\n- listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])\n- listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])\n- listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])\n+ args$calcCiS=as.logical(args$calcCiS)\n+ args$calcIso=as.logical(args$calcIso)\n+ args$calcCaS=as.logical(args$calcCaS)\n \n # common parameters\n- listArguments4annotate = list(object=xset,\n- nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],\n- maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],\n- ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],\n- polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])\n+ args4annotate = list(object=xset,\n+ nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm,\n+ maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac,\n+ ppm=args$ppm,mzabs=args$mzabs,quick=args$quick,\n+ polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval)\n \n # quick == FALSE\n- if(listArguments[["quick"]]==FALSE) {\n- listArguments4annotate = append(listArguments4annotate,\n- list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],\n- calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]]))\n+ if(args$quick==FALSE) {\n+ args4annotate = append(args4annotate,\n+ list(graphMethod=args$graphMethod,cor_eic_t'..b'lue), ]\n }\n }\n@@ -171,7 +217,9 @@\n }\n \n \n-combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){\n+combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,\n+ pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0,\n+ numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){\n \n #Load the two Rdata to extract the xset objects from positive and negative mode\n cat("\\tObject xset from positive mode\\n")\n@@ -198,11 +246,9 @@\n \n if(pos){\n xa=xaP\n- listOFlistArgumentsP=listOFlistArguments\n mode="neg. Mode"\n } else {\n xa=xaN\n- listOFlistArgumentsN=listOFlistArguments\n mode="pos. Mode"\n }\n \n@@ -239,22 +285,22 @@\n }\n \n # This function get the raw file path from the arguments\n-getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {\n- if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]\n- if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]\n- if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]\n+getRawfilePathFromArguments <- function(singlefile, zipfile, args) {\n+ if (!is.null(args$zipfile)) zipfile = args$zipfile\n+ if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive\n+ if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative\n \n- if (!is.null(listArguments[["singlefile_galaxyPath"]])) {\n- singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];\n- singlefile_sampleNames = listArguments[["singlefile_sampleName"]]\n+ if (!is.null(args$singlefile_galaxyPath)) {\n+ singlefile_galaxyPaths = args$singlefile_galaxyPath;\n+ singlefile_sampleNames = args$singlefile_sampleName\n }\n- if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {\n- singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];\n- singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]\n+ if (!is.null(args$singlefile_galaxyPathPositive)) {\n+ singlefile_galaxyPaths = args$singlefile_galaxyPathPositive;\n+ singlefile_sampleNames = args$singlefile_sampleNamePositive\n }\n- if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {\n- singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];\n- singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]\n+ if (!is.null(args$singlefile_galaxyPathNegative)) {\n+ singlefile_galaxyPaths = args$singlefile_galaxyPathNegative;\n+ singlefile_sampleNames = args$singlefile_sampleNameNegative\n }\n if (exists("singlefile_galaxyPaths")){\n singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))\n@@ -267,10 +313,13 @@\n singlefile[[singlefile_sampleName]] = singlefile_galaxyPath\n }\n }\n- for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {\n- listArguments[[argument]]=NULL\n+ for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",\n+ "singlefile_galaxyPath", "singlefile_sampleName",\n+ "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",\n+ "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {\n+ args[[argument]]=NULL\n }\n- return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))\n+ return(list(zipfile=zipfile, singlefile=singlefile, args=args))\n }\n \n \n' |
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| diff -r 73d82de36369 -r cb923396e70f macros.xml --- a/macros.xml Tue Oct 09 06:03:01 2018 -0400 +++ b/macros.xml Thu Aug 29 11:38:21 2019 -0400 |
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| @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4_2">r-snow</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="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="1.3.23">graphicsmagick</requirement> + <requirement type="package" version="1.3.31">graphicsmagick</requirement> </requirements> </xml> <xml name="stdio"> @@ -16,9 +15,7 @@ </stdio> </xml> - <token name="@COMMAND_CAMERA_SCRIPT@"> - LC_ALL=C Rscript $__tool_directory__/CAMERA.r - </token> + <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token> <!-- raw file load for planemo test --> <token name="@COMMAND_FILE_LOAD@"> |
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| diff -r 73d82de36369 -r cb923396e70f planemo_test.sh --- a/planemo_test.sh Tue Oct 09 06:03:01 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,29 +0,0 @@ -# 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 - -#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 - -#All 1 test(s) executed passed. -#abims_CAMERA_annotateDiffreport[0]: passed - - -# -- Use of shed_test -planemo shed_test --install_galaxy -t testtoolshed - -#All 1 test(s) executed passed. -#testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: passed |
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| diff -r 73d82de36369 -r cb923396e70f repository_dependencies.xml --- a/repository_dependencies.xml Tue Oct 09 06:03:01 2018 -0400 +++ b/repository_dependencies.xml Thu Aug 29 11:38:21 2019 -0400 |
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| @@ -1,5 +1,5 @@ -<?xml version="1.0"?> +<?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="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="4a51ab3d8ecf" name="rdata_camera_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> \ No newline at end of file |
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| diff -r 73d82de36369 -r cb923396e70f test-data/.RData |
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| Binary file test-data/.RData has changed |
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| diff -r 73d82de36369 -r cb923396e70f test-data/CMD.mac.sh --- a/test-data/CMD.mac.sh Tue Oct 09 06:03:01 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -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 73d82de36369 -r cb923396e70f test-data/Rplots.pdf |
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| diff -r 73d82de36369 -r cb923396e70f test-data/dataMatrixOutput.txt --- a/test-data/dataMatrixOutput.txt Tue Oct 09 06:03:01 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,6333 +0,0 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