| Previous changeset 5:588b0a7ae4b0 (2016-02-22) Next changeset 7:451ff602a957 (2016-04-25) |
|
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 |
|
modified:
README.rst abims_xcms_xcmsSet.xml tool_dependencies.xml |
|
added:
lib.r macros.xml planemo_test.sh test-data/sacuri_current_root.zip test-data/sacuri_dir_root.log.txt test-data/sacuri_dir_root.zip xcms.r |
|
removed:
planemo.sh test-data/log.txt test-data/sacuri.zip test-data/sampleMetadata.tsv test-data/xset.BPCs_raw.pdf test-data/xset.RData test-data/xset.TICs_raw.pdf |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a README.rst --- a/README.rst Mon Feb 22 16:25:05 2016 -0500 +++ b/README.rst Fri Apr 08 10:38:52 2016 -0400 |
| b |
| @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 2.0.8 - 06/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + **Version 2.0.7 - 10/02/2016** @@ -16,7 +20,7 @@ - UPDATE: refactoring to feed the new report tool -**Version 2.0.2 - 18/01/2016 +**Version 2.0.2 - 18/01/2016** - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases. @@ -33,3 +37,13 @@ - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. - IMPROVEMENT: parameter labels have changed to facilitate their reading. + + +Test Status +----------- + +Planemo test using conda: passed + +Planemo test using source env.sh: passed + +Planemo shed_test : passed \ No newline at end of file |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Mon Feb 22 16:25:05 2016 -0500 +++ b/abims_xcms_xcmsSet.xml Fri Apr 08 10:38:52 2016 -0400 |
| [ |
| @@ -1,20 +1,16 @@ -<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.7"> +<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.8"> <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> - <requirements> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="binary">Rscript</requirement> - <requirement type="package" version="1.44.0">xcms</requirement> - <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> - </requirements> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> <command><![CDATA[ - xcms.r + @COMMAND_XCMS_SCRIPT@ #if $inputs.input == "lib": library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library #elif $inputs.input == "zip_file": @@ -33,16 +29,16 @@ #if $methods.method == "centWave": ppm $methods.ppm peakwidth "c($methods.peakwidth)" - #if $methods.options_scanrange.option == "show": + #if $methods.options_scanrange.option == "show": scanrange "c($methods.options_scanrange.scanrange)" - #end if - #if $methods.options_c.option == "show": - mzdiff $methods.options_c.mzdiff - snthresh $methods.options_c.snthresh - integrate $methods.options_c.integrate - noise $methods.options_c.noise - prefilter "c($methods.options_c.prefilter)" - #end if + #end if + #if $methods.options_c.option == "show": + mzdiff $methods.options_c.mzdiff + snthresh $methods.options_c.snthresh + integrate $methods.options_c.integrate + noise $methods.options_c.noise + prefilter "c($methods.options_c.prefilter)" + #end if #elif $methods.method == "matchedFilter": step $methods.step fwhm $methods.fwhm @@ -62,11 +58,7 @@ scales "c($methods.scales)" SNR.method "$methods.SNR_method" #end if - ; - return=\$?; - mv log.txt $log; - cat $log; - sh -c "exit \$return" + @COMMAND_LOG_EXIT@ ]]></command> <inputs> @@ -192,25 +184,38 @@ <tests> <test> - <param name="inputs.input" value="zip_file" /> - <param name="inputs.zip_file" value="sacuri.zip" /> - <param name="methods.method" value="matchedFilter" /> - <param name="methods.step" value="0.01" /> - <param name="methods.fwhm" value="4" /> - <param name="methods.options_m.option" value="show" /> - <param name="methods.options_m.max" value="50" /> - <param name="methods.options_m.snthresh" value="1" /> - <param name="methods.options_m.steps" value="2" /> - <!--<output name="xsetRData" file="xset.RData" />--> - <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />--> - <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />--> - <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />--> + <param name="inputs|input" value="zip_file" /> + <param name="inputs|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> + <param name="methods|method" value="matchedFilter" /> + <param name="methods|step" value="0.01" /> + <param name="methods|fwhm" value="4" /> + <param name="methods|options_m|option" value="show" /> + <param name="methods|options_m|max" value="50" /> + <param name="methods|options_m|snthresh" value="1" /> + <param name="methods|options_m|steps" value="2" /> <output name="log"> <assert_contents> - <has_text text="object with 9 samples" /> - <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" /> - <has_text text="Mass range: 50.0019-999.9863 m/z" /> - <has_text text="Peaks: 135846 (about 15094 per sample)" /> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" /> + <has_text text="Mass range: 50.0021-999.9863 m/z" /> + <has_text text="Peaks: 59359 (about 14840 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputs|input" value="zip_file" /> + <param name="inputs|zip_file" value="sacuri_current_root.zip" ftype="zip" /> + <param name="methods|method" value="centWave" /> + <param name="methods|ppm" value="25" /> + <param name="methods|peakwidth" value="20,50" /> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" /> + <has_text text="Mass range: 57.9756-593.4086 m/z" /> + <has_text text="Peaks: 1535 (about 384 per sample)" /> <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: bio, blank" /> </assert_contents> @@ -220,17 +225,7 @@ <help><![CDATA[ -.. 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@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] - - | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. - ---------------------------------------------------- +@HELP_AUTHORS@ ============ Xcms.xcmsSet @@ -463,6 +458,10 @@ Changelog/News -------------- +**Version 2.0.8 - 06/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + **Version 2.0.7 - 10/02/2016** @@ -474,7 +473,7 @@ - UPDATE: refactoring of internal management of inputs/outputs -- UPDATE: refactoring to feed the new report tool +- TEST: refactoring to feed the new report tool **Version 2.0.2 - 18/01/2016 @@ -497,10 +496,5 @@ ]]></help> - - <citations> - <citation type="doi">10.1021/ac051437y</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> - + <expand macro="citation" /> </tool> |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a lib.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Fri Apr 08 10:38:52 2016 -0400 |
| [ |
| b'@@ -0,0 +1,400 @@\n+# lib.r version="2.0.1"\n+#Authors ABiMS TEAM\n+#Lib.r for Galaxy Workflow4Metabo\n+#version 2.2\n+#Based on lib.r 2.1\n+#Modifications made by Guitton Yann \n+#correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet\n+#Note if scanrange is used a warning is prompted in R console but do not stop PDF generation\n+\n+\n+\n+\n+#@author Y. Guitton\n+getBPC <- function(file,rtcor=NULL, ...) {\n+ object <- xcmsRaw(file)\n+ sel <- profRange(object, ...)\n+ cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))\n+ #plotChrom(xcmsRaw(file), base=T)\n+}\n+\n+#@author Y. Guitton\n+getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {\n+ cat("Creating BIC pdf...\\n")\n+\n+ if (is.null(xcmsSet)) {\n+ cat("Enter an xcmsSet \\n")\n+ stop()\n+ } else {\n+ files <- filepaths(xcmsSet)\n+ }\n+\n+ class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class\n+\n+ classnames<-vector("list",length(class))\n+ for (i in 1:length(class)){\n+ classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])\n+ }\n+\n+ N <- dim(phenoData(xcmsSet))[1]\n+\n+ TIC <- vector("list",N)\n+\n+\n+ for (j in 1:N) {\n+\n+ TIC[[j]] <- getBPC(files[j])\n+ #good for raw \n+ # seems strange for corrected\n+ #errors if scanrange used in xcmsSetgeneration\n+ if (!is.null(xcmsSet) && rt == "corrected")\n+ rtcor <- xcmsSet@rt$corrected[[j]] else\n+ rtcor <- NULL\n+ \n+ TIC[[j]] <- getBPC(files[j],rtcor=rtcor)\n+ # TIC[[j]][,1]<-rtcor\n+ }\n+\n+\n+\n+ pdf(pdfname,w=16,h=10)\n+ cols <- rainbow(N)\n+ lty = 1:N\n+ pch = 1:N\n+ #search for max x and max y in BPCs\n+ xlim = range(sapply(TIC, function(x) range(x[,1])))\n+ ylim = range(sapply(TIC, function(x) range(x[,2])))\n+ ylim = c(-ylim[2], ylim[2])\n+\n+\n+ ##plot start\n+ \n+ if (length(class)>2){\n+ for (k in 1:(length(class)-1)){\n+ for (l in (k+1):length(class)){\n+ #print(paste(class[k],"vs",class[l],sep=" ")) \n+ plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \\n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")\n+ colvect<-NULL\n+ for (j in 1:length(classnames[[k]])) {\n+ tic <- TIC[[classnames[[k]][j]]]\n+ # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")\n+ points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")\n+ colvect<-append(colvect,cols[classnames[[k]][j]])\n+ }\n+ for (j in 1:length(classnames[[l]])) {\n+ # i=class2names[j]\n+ tic <- TIC[[classnames[[l]][j]]]\n+ points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")\n+ colvect<-append(colvect,cols[classnames[[l]][j]])\n+ }\n+ legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)\n+ }\n+ }\n+ }#end if length >2\n+\n+ if (length(class)==2){\n+ k=1\n+ l=2\n+ colvect<-NULL\n+ plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \\n","BPCs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")\n+\n+ for (j in 1:length(classnames[[k]])) {\n+\n+ tic <- TIC[[classnames[[k]][j]]]\n+ # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")\n+ points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")\n+ colvect<-append(colvect,cols[classnames[[k]][j]])\n+ }\n+ for (j in 1:length(classnames[[l]])) {\n+ # i=class2names[j]\n+ tic <- TIC[[classnames[[l]][j]]]\n+ points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")\n+ colvect<-append(colvect,cols[classnames[[l]][j]])\n+ }\n+ legen'..b'}\n+\n+\n+##\n+## This function check if xcms will found all the files\n+##\n+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM\n+checkFilesCompatibilityWithXcms <- function(directory) {\n+ cat("Checking files filenames compatibilities with xmcs...\\n")\n+ # WHAT XCMS WILL FIND\n+ filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n+ filepattern <- paste(paste("\\\\.", filepattern, "$", sep = ""),collapse = "|")\n+ info <- file.info(directory)\n+ listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)\n+ files <- c(directory[!info$isdir], listed)\n+ files_abs <- file.path(getwd(), files)\n+ exists <- file.exists(files_abs)\n+ files[exists] <- files_abs[exists]\n+ files[exists] <- sub("//","/",files[exists])\n+\n+ # WHAT IS ON THE FILESYSTEM\n+ filesystem_filepaths=system(paste("find $PWD/",directory," -not -name \'\\\\.*\' -not -path \'*conda-env*\' -type f -name \\"*\\"", sep=""), intern=T)\n+ filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]\n+\n+ # COMPARISON\n+ if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { \n+ write("\\n\\nERROR: List of the files which will not be imported by xcmsSet",stderr())\n+ write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())\n+ stop("\\n\\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")\n+\n+ }\n+}\n+\n+\n+\n+##\n+## This function check if XML contains special caracters. It also checks integrity and completness.\n+##\n+#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM\n+checkXmlStructure <- function (directory) {\n+ cat("Checking XML structure...\\n")\n+\n+ cmd=paste("IFS=$\'\\n\'; for xml in $(find",directory,"-not -name \'\\\\.*\' -not -path \'*conda-env*\' -type f -iname \'*.*ml*\'); do if [ $(xmllint --nonet --noout \\"$xml\\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")\n+ capture=system(cmd,intern=TRUE)\n+\n+ if (length(capture)>0){\n+ #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)\n+ write("\\n\\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())\n+ write(capture, stderr())\n+ stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")\n+ }\n+ \n+}\n+\n+\n+##\n+## This function check if XML contain special characters\n+##\n+#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM\n+deleteXmlBadCharacters<- function (directory) {\n+ cat("Checking Non ASCII characters in the XML...\\n")\n+\n+ processed=F\n+ l=system( paste("find",directory, "-not -name \'\\\\.*\' -not -path \'*conda-env*\' -type f -iname \'*.*ml*\'"),intern=TRUE) \n+ for (i in l){\n+ cmd=paste("LC_ALL=C grep \'[^ -~]\' \\"",i,"\\"",sep="")\n+ capture=suppressWarnings(system(cmd,intern=TRUE))\n+ if (length(capture)>0){\n+ cmd=paste("perl -i -pe \'s/[^[:ascii:]]//g;\'",i)\n+ print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )\n+ c=system(cmd,intern=TRUE)\n+ capture=""\n+ processed=T \n+ }\n+ }\n+ if (processed) cat("\\n\\n")\n+ return(processed)\n+}\n+\n+\n+## \n+## This function will compute MD5 checksum to check the data integrity\n+##\n+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n+getMd5sum <- function (directory) {\n+ cat("Compute md5 checksum...\\n")\n+ # WHAT XCMS WILL FIND\n+ filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n+ filepattern <- paste(paste("\\\\.", filepattern, "$", sep = ""),collapse = "|")\n+ info <- file.info(directory)\n+ listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)\n+ files <- c(directory[!info$isdir], listed)\n+ exists <- file.exists(files)\n+ files <- files[exists]\n+\n+ library(tools)\n+\n+ #cat("\\n\\n")\n+\n+ return(as.matrix(md5sum(files)))\n+}\n+\n' |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Apr 08 10:38:52 2016 -0400 |
| [ |
| @@ -0,0 +1,51 @@ +<?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="1.44.0">bioconductor-xcms</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + </xml> + + <token name="@COMMAND_XCMS_SCRIPT@"> + LANG=C Rscript $__tool_directory__/xcms.r + </token> + + <token name="@COMMAND_LOG_EXIT@"> + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + </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/ac051437y</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a planemo.sh --- a/planemo.sh Mon Feb 22 16:25:05 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,1 +0,0 @@ -planemo shed_init -f --name=xcms_xcms_set --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nFiltration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics" |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Fri Apr 08 10:38:52 2016 -0400 |
| [ |
| @@ -0,0 +1,18 @@ +planemo conda_init +planemo conda_install . +planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev" + +#All 2 test(s) executed passed. +#abims_xcms_xcmsSet[0]: passed +#abims_xcms_xcmsSet[1]: passed + + + + +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-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh +planemo test --install_galaxy --galaxy_branch "dev" + +#All 2 test(s) executed passed. +#abims_xcms_xcmsSet[0]: passed +#abims_xcms_xcmsSet[1]: passed \ No newline at end of file |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/log.txt --- a/test-data/log.txt Mon Feb 22 16:25:05 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,56 +0,0 @@ - PACKAGE INFO -parallel 3.1.1 -BiocGenerics 0.12.1 -Biobase 2.26.0 -Rcpp 0.11.5 -mzR 2.0.0 -igraph 0.7.1 -xcms 1.42.0 -snow 0.3.13 -batch 1.1.4 - - - ARGUMENTS INFO -zipfile /w/galaxy/galaxy4metabolomics/galaxy-dist/database/files/041/dataset_41794.dat -xfunction xcmsSet -nSlaves 8 -method matchedFilter -step 0.01 -fwhm 4 -max 50 -snthresh 1 -steps 2 - - - INFILE PROCESSING INFO - - - MAIN PROCESSING INFO -Starting snow cluster with 8 local sockets. -Detecting features in file # 1 : HU_neg_028.mzXML -Detecting features in file # 2 : HU_neg_060.mzXML -Detecting features in file # 3 : HU_neg_051.mzXML -Detecting features in file # 4 : HU_neg_017.mzXML -Detecting features in file # 5 : HU_neg_034.mzXML -Detecting features in file # 6 : Blanc09.mzXML -Detecting features in file # 7 : Blanc06.mzXML -Detecting features in file # 8 : Blanc12.mzXML -Detecting features in file # 9 : Blanc04.mzXML - - - XSET OBJECT INFO -An "xcmsSet" object with 9 samples - -Time range: 0.7-1140 seconds (0-19 minutes) -Mass range: 50.0019-999.9863 m/z -Peaks: 135846 (about 15094 per sample) -Peak Groups: 0 -Sample classes: bio, blank - -Profile settings: method = bin - step = 0.01 - -Memory usage: 13.8 MB - - - DONE |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/sacuri.zip |
| b |
| Binary file test-data/sacuri.zip has changed |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/sacuri_current_root.zip |
| b |
| Binary file test-data/sacuri_current_root.zip has changed |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/sacuri_dir_root.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sacuri_dir_root.log.txt Fri Apr 08 10:38:52 2016 -0400 |
| b |
| b'@@ -0,0 +1,67 @@\n+\tPACKAGE INFO\n+parallel\t3.2.2\n+BiocGenerics\t0.16.1\n+Biobase\t2.30.0\n+Rcpp\t0.12.2\n+mzR\t2.4.1\n+xcms\t1.44.0\n+snow\t0.4.1\n+batch\t1.1.4\n+\n+\n+\tARGUMENTS INFO\n+zipfile\t/tmp/tmpAmhDSv/files/000/dataset_1.dat\n+xfunction\txcmsSet\n+xsetRdataOutput\t/tmp/tmpAmhDSv/files/000/dataset_2.dat\n+sampleMetadataOutput\t/tmp/tmpAmhDSv/files/000/dataset_3.dat\n+ticspdf\t/tmp/tmpAmhDSv/files/000/dataset_4.dat\n+bicspdf\t/tmp/tmpAmhDSv/files/000/dataset_5.dat\n+nSlaves\t1\n+method\tmatchedFilter\n+step\t0.01\n+fwhm\t4\n+max\t50\n+snthresh\t1\n+steps\t2\n+\n+\n+\tINFILE PROCESSING INFO\n+\n+\n+\tARGUMENTS PROCESSING INFO\n+files_root_directory\t sacuri \n+Compute md5 checksum...\n+Checking XML structure...\n+Checking files filenames compatibilities with xmcs...\n+\n+\n+\tMAIN PROCESSING INFO\n+55:579 60:1264 65:1988 70:2602 75:3287 80:3894 85:4629 90:5499 95:6174 100:6672 105:7194 110:7737 115:8205 120:8673 125:9117 130:9532 135:9973 140:10562 145:10945 150:11380 155:11788 160:12163 165:12477 170:12835 175:13276 180:13632 185:14142 190:14489 195:15022 200:15360 205:15716 210:15992 215:16297 220:16669 225:16895 230:17227 235:17487 240:17657 245:17956 250:18238 255:18464 260:18779 265:18969 270:19194 275:19503 280:19798 285:20041 290:20282 295:20498 300:20673 305:21027 310:21220 315:21403 320:21881 325:22431 330:22630 335:22775 340:22969 345:23144 350:23282 355:23425 360:24001 365:24131 370:24242 375:24362 380:24475 385:24580 390:24763 395:25006 400:25190 405:25308 410:25446 415:25555 420:25648 425:25761 430:25962 435:26057 440:26172 445:26260 450:26343 455:26414 460:26608 465:26720 470:26827 475:26979 480:27048 485:27126 490:27218 495:27272 500:27341 505:27433 510:27487 515:27535 520:27600 525:27758 530:27820 535:27896 540:27940 545:28085 550:28141 555:28298 560:28711 565:28732 570:28760 575:28792 580:28822 585:28995 590:29019 595:29059 600:29090 605:29119 610:29151 615:29182 620:29202 625:29238 630:29266 635:29294 640:29317 645:29472 650:29494 655:29599 660:29628 665:29781 670:29812 675:29868 680:29895 685:29923 690:29953 695:29973 700:30032 705:30048 710:30069 715:30089 720:30107 725:30128 730:30144 735:30168 740:30286 745:30312 750:30331 755:30369 760:30402 765:30420 770:30438 775:30584 780:30620 785:30647 790:30666 795:30682 800:30701 805:30712 810:30785 815:30801 820:30816 825:30831 830:30945 835:30979 840:31004 845:31102 850:31114 855:31132 860:31147 865:31166 870:31175 875:31205 880:31227 885:31253 890:31264 895:31280 900:31298 905:31314 910:31325 915:31337 920:31351 925:31370 930:31389 935:31405 940:31416 945:31442 950:31453 955:31470 960:31486 965:31680 970:31794 975:31803 980:31811 985:31836 990:32026 995:32126 1000:32142 \n+55:826 60:1707 65:2578 70:3373 75:4271 80:5020 85:5907 90:6893 95:7729 100:8434 105:9094 110:9712 115:10298 120:10911 125:11430 130:12005 135:12573 140:13234 145:13750 150:14314 155:14841 160:15333 165:15894 170:16323 175:16847 180:17319 185:17867 190:18337 195:18957 200:19402 205:19925 210:20275 215:20746 220:21271 225:21607 230:22062 235:22473 240:22748 245:23187 250:23559 255:23845 260:24284 265:24628 270:24973 275:25315 280:25726 285:26019 290:26327 295:26632 300:26886 305:27300 310:27579 315:27880 320:28450 325:29107 330:29377 335:29609 340:29860 345:30141 350:30369 355:30586 360:31214 365:31446 370:31656 375:31860 380:32067 385:32210 390:32451 395:32690 400:32909 405:33093 410:33312 415:33488 420:33687 425:33837 430:34074 435:34229 440:34403 445:34541 450:34702 455:34798 460:35015 465:35207 470:35390 475:35528 480:35633 485:35754 490:35880 495:35964 500:36076 505:36165 510:36251 515:36336 520:36439 525:36588 530:36699 535:36810 540:36882 545:37060 550:37124 555:37263 560:37718 565:37789 570:37829 575:37878 580:37915 585:38016 590:38054 595:38102 600:38137 605:38188 610:38237 615:38277 620:38312 625:38359 630:38387 635:38413 640:38450 645:38558 650:38590 655:38714 660:38749 665:38864 670:38914 675:38967 680:39003 685:39038 690:39073 695:39096 700:39199 705:39227 710:39256 715:39279 720:39302 725:39334 730:39358 735:39388 740:39513 745:39537'..b'0:9632 155:9960 160:10258 165:10541 170:10816 175:11141 180:11384 185:11827 190:12048 195:12370 200:12608 205:12929 210:13142 215:13337 220:13642 225:13802 230:14032 235:14204 240:14349 245:14614 250:14773 255:14935 260:15217 265:15344 270:15512 275:15763 280:15966 285:16095 290:16255 295:16456 300:16589 305:16806 310:16956 315:17091 320:17476 325:17978 330:18165 335:18251 340:18393 345:18517 350:18606 355:18739 360:19210 365:19275 370:19358 375:19420 380:19510 385:19577 390:19668 395:19833 400:19955 405:20040 410:20154 415:20244 420:20323 425:20414 430:20577 435:20639 440:20724 445:20785 450:20835 455:20897 460:21073 465:21160 470:21235 475:21428 480:21486 485:21538 490:21599 495:21640 500:21685 505:21738 510:21773 515:21798 520:21863 525:22005 530:22044 535:22121 540:22162 545:22286 550:22340 555:22493 560:22814 565:22842 570:22869 575:22895 580:22927 585:23067 590:23090 595:23119 600:23134 605:23172 610:23197 615:23223 620:23242 625:23275 630:23304 635:23314 640:23339 645:23465 650:23490 655:23600 660:23619 665:23756 670:23781 675:23849 680:23870 685:23895 690:23910 695:23929 700:23992 705:24015 710:24026 715:24044 720:24068 725:24089 730:24122 735:24146 740:24242 745:24259 750:24280 755:24307 760:24330 765:24352 770:24373 775:24493 780:24514 785:24551 790:24563 795:24584 800:24605 805:24637 810:24684 815:24704 820:24715 825:24723 830:24736 835:24763 840:24854 845:24938 850:24950 855:24968 860:24983 865:25000 870:25019 875:25030 880:25046 885:25067 890:25084 895:25100 900:25119 905:25132 910:25141 915:25153 920:25170 925:25184 930:25199 935:25211 940:25224 945:25240 950:25251 955:25266 960:25278 965:25437 970:25548 975:25560 980:25568 985:25580 990:25784 995:25822 \n+55:568 60:1154 65:1793 70:2433 75:3064 80:3635 85:4363 90:5039 95:5627 100:6077 105:6641 110:7124 115:7603 120:8076 125:8439 130:8836 135:9206 140:9628 145:9963 150:10288 155:10623 160:10937 165:11304 170:11676 175:12092 180:12358 185:12768 190:13022 195:13435 200:13746 205:14079 210:14229 215:14412 220:14688 225:14901 230:15155 235:15314 240:15475 245:15750 250:15938 255:16115 260:16396 265:16512 270:16704 275:16893 280:17127 285:17336 290:17484 295:17668 300:17788 305:18044 310:18177 315:18318 320:18785 325:19242 330:19399 335:19491 340:19646 345:19785 350:19886 355:19994 360:20481 365:20574 370:20675 375:20743 380:20827 385:20903 390:21012 395:21202 400:21349 405:21433 410:21527 415:21590 420:21649 425:21741 430:21888 435:21942 440:21998 445:22067 450:22121 455:22169 460:22293 465:22371 470:22476 475:22629 480:22666 485:22706 490:22765 495:22820 500:22881 505:22934 510:22988 515:23039 520:23087 525:23185 530:23226 535:23293 540:23332 545:23463 550:23513 555:23674 560:24058 565:24076 570:24095 575:24132 580:24156 585:24262 590:24278 595:24313 600:24336 605:24360 610:24396 615:24421 620:24459 625:24479 630:24498 635:24521 640:24542 645:24692 650:24712 655:24831 660:24853 665:24976 670:24991 675:25048 680:25063 685:25079 690:25095 695:25114 700:25163 705:25184 710:25202 715:25213 720:25227 725:25250 730:25276 735:25289 740:25384 745:25400 750:25416 755:25458 760:25483 765:25508 770:25530 775:25654 780:25671 785:25692 790:25715 795:25742 800:25752 805:25763 810:25832 815:25845 820:25862 825:25875 830:25890 835:25905 840:26020 845:26094 850:26108 855:26134 860:26150 865:26163 870:26174 875:26185 880:26200 885:26212 890:26225 895:26236 900:26250 905:26262 910:26279 915:26287 920:26299 925:26317 930:26325 935:26339 940:26356 945:26367 950:26381 955:26392 960:26404 965:26592 970:26701 975:26720 980:26743 985:26759 990:26969 995:26990 \n+\n+\n+null device \n+ 1 \n+Creating the sampleMetadata file...\n+Creating TIC pdf...\n+Creating BIC pdf...\n+\n+\n+\tXSET OBJECT INFO\n+An "xcmsSet" object with 4 samples\n+\n+Time range: 0.7-1139.7 seconds (0-19 minutes)\n+Mass range: 50.0021-999.9863 m/z\n+Peaks: 59359 (about 14840 per sample)\n+Peak Groups: 0 \n+Sample classes: bio, blank \n+\n+Profile settings: method = bin\n+ step = 0.01\n+\n+Memory usage: 6.02 MB\n+\n+\n+\tDONE\n' |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/sacuri_dir_root.zip |
| b |
| Binary file test-data/sacuri_dir_root.zip has changed |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/sampleMetadata.tsv --- a/test-data/sampleMetadata.tsv Mon Feb 22 16:25:05 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -sampleMetadata class polarity -HU_neg_028 bio negative -HU_neg_060 bio negative -HU_neg_051 bio negative -HU_neg_017 bio negative -HU_neg_034 bio negative -Blanc09 blank negative -Blanc06 blank negative -Blanc12 blank negative -Blanc04 blank negative |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/xset.BPCs_raw.pdf |
| b |
| Binary file test-data/xset.BPCs_raw.pdf has changed |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/xset.RData |
| b |
| Binary file test-data/xset.RData has changed |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a test-data/xset.TICs_raw.pdf |
| b |
| Binary file test-data/xset.TICs_raw.pdf has changed |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 22 16:25:05 2016 -0500 +++ b/tool_dependencies.xml Fri Apr 08 10:38:52 2016 -0400 |
| b |
| @@ -1,12 +1,9 @@ <?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" /> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="xcms" version="1.44.0"> - <repository changeset_revision="4443617bdd85" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="xcms_w4m_script" version="2.2.0"> - <repository changeset_revision="115cf2b43a3c" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="bioconductor-xcms" version="1.44.0"> + <repository changeset_revision="58ebb405a3d6" name="package_bioconductor_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
| b |
| diff -r 588b0a7ae4b0 -r 0888f7ef739a xcms.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms.r Fri Apr 08 10:38:52 2016 -0400 |
| [ |
| @@ -0,0 +1,246 @@ +#!/usr/bin/env Rscript +# xcms.r version="2.2.0" +#Authors ABIMS TEAM +#BPC Addition from Y.guitton + + +# ----- LOG FILE ----- +log_file=file("log.txt", open = "wt") +sink(log_file) +sink(log_file, type = "output") + + +# ----- PACKAGE ----- +cat("\tPACKAGE INFO\n") +#pkgs=c("xcms","batch") +pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") +for(pkg in pkgs) { + suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + cat(pkg,"\t",as.character(packageVersion(pkg)),"\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"); + + +# ----- ARGUMENTS PROCESSING ----- +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 +} + +#Import the different functions +source_local("lib.r") + +cat("\n\n") + +#Import the different functions + +# ----- PROCESSING INFILE ----- +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 +} + +sampleMetadataOutput = "sampleMetadata.tsv" +if (!is.null(listArguments[["sampleMetadataOutput"]])){ + sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL +} + + + + +if (thefunction %in% c("xcmsSet","retcor")) { + ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL + bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL +} + +#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 +} + +if (!is.null(listArguments[["library"]])){ + directory=listArguments[["library"]]; listArguments[["library"]]=NULL + if(!file.exists(directory)){ + error_message=paste("Cannot access the directory:",directory,". Please verify if the directory exists or not.") + print(error_message) + stop(error_message) + } +} + +# We unzip automatically the chromatograms from the zip files. +if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { + 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) + } + + #list all file in the zip file + #zip_files=unzip(zipfile,list=T)[,"Name"] + + + #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)$isdir] + directory = "." + if (length(directories) == 1) directory = directories + + cat("files_root_directory\t",directory,"\n") + + # + md5sumList=list("origin"=getMd5sum(directory)) + + # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files. + # Remove because can create issue with some clean files + #@TODO: fix me + #if (deleteXmlBadCharacters(directory)) { + # md5sumList=list("removalBadCharacters"=getMd5sum(directory)) + #} + + } +} + +#addition of the directory to the list of arguments in the first position +if (thefunction == "xcmsSet") { + checkXmlStructure(directory) + checkFilesCompatibilityWithXcms(directory) + listArguments=append(directory, listArguments) +} + + +#addition of xset object to the list of arguments in the first position +if (exists("xset")){ + listArguments=append(list(xset), listArguments) +} + +cat("\n\n") + + + + + + +# ----- MAIN PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + + +#Verification of a group step before doing the fillpeaks job. + +if (thefunction == "fillPeaks") { + res=try(is.null(groupnames(xset))) + if (class(res) == "try-error"){ + error<-geterrmessage() + write(error, stderr()) + stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step") + } + +} + +#change the default display settings +#dev.new(file="Rplots.pdf", width=16, height=12) +pdf(file=rplotspdf, width=16, height=12) +if (thefunction == "group") { + par(mfrow=c(2,2)) +} +#else if (thefunction == "retcor") { +#try to change the legend display +# par(xpd=NA) +# par(xpd=T, mar=par()$mar+c(0,0,0,4)) +#} + + +#execution of the function "thefunction" with the parameters given in "listArguments" +xset = do.call(thefunction, listArguments) + + +cat("\n\n") + +dev.off() #dev.new(file="Rplots.pdf", width=16, height=12) + +if (thefunction == "xcmsSet") { + + #transform the files absolute pathways into relative pathways + xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) + + if(exists("zipfile") && (zipfile!="")) { + + #Modify the samples names (erase the path) + for(i in 1:length(sampnames(xset))){ + + sample_name=unlist(strsplit(sampnames(xset)[i], "/")) + sample_name=sample_name[length(sample_name)] + sample_name= unlist(strsplit(sample_name,"[.]"))[1] + sampnames(xset)[i]=sample_name + + } + + } + +} + +# -- TIC -- +if (thefunction == "xcmsSet") { + sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) + getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw") + getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf) +} else if (thefunction == "retcor") { + getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected") + getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf) +} + +cat("\n\n") + + +# ----- EXPORT ----- + +cat("\tXSET OBJECT INFO\n") +print(xset) +#delete the parameters to avoid the passage to the next tool in .RData image + + +#saving R data in .Rdata file to save the variables used in the present tool +objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList") +save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) + +cat("\n\n") + + +cat("\tDONE\n") + |