| Previous changeset 9:2c1d7df89cf6 (2017-01-30) Next changeset 11:9e45e1c404a4 (2017-05-19) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 |
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modified:
README.rst abims_xcms_group.xml lib.r macros.xml static/images/xcms_group_workflow.png xcms.r |
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added:
test-data/MM-single.xset.merged.RData test-data/faahKO-single-class.xset.merged.RData test-data/faahKO-single.xset.merged.RData test-data/faahKO-single.xset.merged.group.retcor.RData test-data/faahKO.xset.group.dataMatrix.tsv test-data/faahKO.xset.group.variableMetadata.tsv |
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removed:
Makefile planemo_test.sh tool_dependencies.xml |
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| diff -r 2c1d7df89cf6 -r c81275aee959 Makefile --- a/Makefile Mon Jan 30 08:53:13 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ -# USAGE: make [install|clean] - -# -------- VARIABLE -------- - -OBJ=xcms_group.tgz -DEP=abims_xcms_group.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 2c1d7df89cf6 -r c81275aee959 README.rst --- a/README.rst Mon Jan 30 08:53:13 2017 -0500 +++ b/README.rst Fri Apr 07 07:35:31 2017 -0400 |
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| @@ -2,13 +2,21 @@ Changelog/News -------------- +**Version 2.1.0 - 07/02/2017** + +- IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate + +- IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger" + +- BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50 + **Version 2.0.6 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 **Version 2.0.5 04/04/2016** -- TEST: refactoring to pass planemo test using conda dependencies +- TEST: refactoring to pass planemo test using conda dependencies **Version 2.0.4 - 10/02/2016** @@ -25,15 +33,3 @@ - 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 - - |
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| diff -r 2c1d7df89cf6 -r c81275aee959 abims_xcms_group.xml --- a/abims_xcms_group.xml Mon Jan 30 08:53:13 2017 -0500 +++ b/abims_xcms_group.xml Fri Apr 07 07:35:31 2017 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="abims_xcms_group" name="xcms.group" version="2.0.6">\n+<tool id="abims_xcms_group" name="xcms.group" version="2.1.0">\n \n <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>\n \n@@ -11,21 +11,21 @@\n \n <command><![CDATA[\n @COMMAND_XCMS_SCRIPT@\n- xfunction group \n- image $image \n+ xfunction group\n+ image \'$image\'\n \n- xsetRdataOutput $xsetRData\n- rplotspdf $rplotsPdf\n+ xsetRdataOutput \'$xsetRData\'\n+ rplotspdf \'$rplotsPdf\'\n \n- method $methods.method sleep 0.001 \n+ method $methods.method sleep 0.001\n #if $methods.method == "density":\n- ## minsamp $methods.minsamp \n- minfrac $methods.minfrac \n- bw $methods.bw \n+ ## minsamp $methods.minsamp\n+ minfrac $methods.minfrac\n+ bw $methods.bw\n mzwid $methods.mzwid\n #if $methods.density_options.option == "show":\n max $methods.density_options.max\n- #end if \n+ #end if\n #elif $methods.method == "mzClust":\n mzppm $methods.mzppm\n mzabs $methods.mzabs\n@@ -37,8 +37,11 @@\n rtCheck $methods.rtCheck\n kNN $methods.kNN\n #end if\n+\n+ @COMMAND_PEAKLIST@\n+\n @COMMAND_LOG_EXIT@\n- ]]></command> \n+ ]]></command>\n \n <inputs>\n <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />\n@@ -53,7 +56,7 @@\n <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />\n <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />\n <!--\n- <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " /> \n+ <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />\n -->\n <conditional name="density_options">\n <param name="option" type="select" label="Advanced options">\n@@ -61,7 +64,7 @@\n <option value="hide" selected="true">hide</option>\n </param>\n <when value="show">\n- <param name="max" type="integer" value="5" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />\n+ <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />\n </when>\n <when value="hide">\n </when>\n@@ -73,27 +76,29 @@\n <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />\n <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" />\n <!--\n- <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " /> \n+ <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />\n -->\n </when>\n <when value="nearest">\n <param name="mzVsRTbalance" typ'..b' <has_text text="object with 2 samples" />\n+ <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />\n+ <has_text text="Mass range: 117.0357-936.7059 m/z" />\n+ <has_text text="Peaks: 236 (about 118 per sample)" />\n+ <has_text text="Peak Groups: 236" />\n+ <has_text text="Sample classes: ." />\n+ </assert_contents>\n+ </output>\n </test>\n <!--<test>\n <param name="image" value="xset.group.retcor.RData"/>\n@@ -174,10 +252,29 @@\n </assert_contents>\n </output>\n </test>\n+ <test>\n+ <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>\n+ <param name="methods|method" value="density"/>\n+ <param name="methods|bw" value="5"/>\n+ <param name="methods|minfrac" value="0.3"/>\n+ <param name="methods|mzwid" value="0.01"/>\n+ <param name="methods|density_options|option" value="show"/>\n+ <param name="methods|density_options|max" value="50"/>\n+ <output name="log">\n+ <assert_contents>\n+ <has_text text="object with 4 samples" />\n+ <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />\n+ <has_text text="Mass range: 200.1-600 m/z" />\n+ <has_text text="Peaks: 9251 (about 2313 per sample)" />\n+ <has_text text="Peak Groups: 8157" />\n+ <has_text text="Sample classes: KO, WT" />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n \n <help><![CDATA[\n- \n+\n @HELP_AUTHORS@\n \n ==========\n@@ -203,6 +300,8 @@\n ========================= ================= =================== ==========\n xcms.xcmsSet xset.RData rdata.xcms.raw RData file\n ------------------------- ----------------- ------------------- ----------\n+xcms.xcmsSet Merger xset.RData rdata.xcms.raw RData file\n+------------------------- ----------------- ------------------- ----------\n xcms.retcor xset.RData rdata.xcms.retcor RData file\n ========================= ================= =================== ==========\n \n@@ -231,7 +330,9 @@\n +---------------------------+-----------------------+\n | Parameter : num + label | Format |\n +===========================+=======================+\n-| 1 : RData file | rdata.xcms.group |\n+| Or : RData file | rdata.xcms.raw |\n++---------------------------+-----------------------+\n+| Or : RData file | rdata.xcms.retcor |\n +---------------------------+-----------------------+\n \n \n@@ -264,15 +365,15 @@\n xset.group.RData: rdata.xcms.group format\n \n | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).\n- \n+\n \n ------\n \n-.. class:: infomark \n+.. class:: infomark\n \n The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool.\n \n- \n+\n ---------------------------------------------------\n \n \n@@ -312,13 +413,21 @@\n Changelog/News\n --------------\n \n+**Version 2.1.0 - 07/02/2017**\n+\n+- IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate\n+\n+- IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"\n+\n+- BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50\n+\n **Version 2.0.6 - 06/07/2016**\n \n - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0\n \n **Version 2.0.5 - 04/04/2016**\n \n-- TEST: refactoring to pass planemo test using conda dependencies \n+- TEST: refactoring to pass planemo test using conda dependencies\n \n \n **Version 2.0.4 - 10/02/2016**\n' |
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| diff -r 2c1d7df89cf6 -r c81275aee959 lib.r --- a/lib.r Mon Jan 30 08:53:13 2017 -0500 +++ b/lib.r Fri Apr 07 07:35:31 2017 -0400 |
| [ |
| b'@@ -27,168 +27,165 @@\n \n #@author G. Le Corguille\n #This function format ions identifiers\n-formatIonIdentifiers <- function(dataData, numDigitsRT=0, numDigitsMZ=0) {\n- return(make.unique(paste0("M",round(dataData[,"mz"],numDigitsMZ),"T",round(dataData[,"rt"],numDigitsRT))))\n+formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {\n+ splitDeco = strsplit(as.character(variableMetadata$name),"_")\n+ idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })\n+ namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))\n+ variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])\n+ return(variableMetadata)\n }\n \n #@author G. Le Corguille\n # value: intensity values to be used into, maxo or intb\n getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {\n- groups <- xset@groups\n- values <- groupval(xset, "medret", value=intval)\n- \n- # renamming of the column rtmed to rt to fit with camera peaklist function output\n- colnames(groups)[colnames(groups)=="rtmed"] <- "rt"\n- colnames(groups)[colnames(groups)=="mzmed"] <- "mz"\n- \n- ids <- formatIonIdentifiers(groups, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)\n- groups = RTSecondToMinute(groups, convertRTMinute)\n+ variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval)\n+ variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix)\n+\n+ dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))]\n \n- rownames(groups) = ids\n- rownames(values) = ids\n+ variableMetadata = variableMetadata_dataMatrix[,!(make.names(colnames(variableMetadata_dataMatrix)) %in% c(make.names(sampnames(xset))))]\n+ variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)\n+ variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)\n \n- #@TODO: add "name" as the first column name\n- #colnames(groups)[1] = "name"\n- #colnames(values)[1] = "name"\n-\n- write.table(groups, file=variableMetadataOutput,sep="\\t",quote=F,row.names = T,col.names = NA)\n- write.table(values, file=dataMatrixOutput,sep="\\t",quote=F,row.names = T,col.names = NA)\n+ write.table(variableMetadata, file=variableMetadataOutput,sep="\\t",quote=F,row.names=F)\n+ write.table(dataMatrix, file=dataMatrixOutput,sep="\\t",quote=F,row.names=F)\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$scanidx,drop=FALSE]))\n- #plotChrom(xcmsRaw(file), base=T)\n+ object <- xcmsRaw(file)\n+ sel <- profRange(object, ...)\n+ cbind(if (is.null(rtcor)) object@scantime[sel$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+ 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+ 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+ phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class\n \n- classnam'..b'as.matrix(md5sum(files)))\n+}\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+\n+ if (!is.null(listArguments[["singlefile_galaxyPath"]])) {\n+ singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];\n+ singlefile_sampleNames = listArguments[["singlefile_sampleName"]]\n+ }\n+ if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {\n+ singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];\n+ singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]\n+ }\n+ if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {\n+ singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];\n+ singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]\n+ }\n+ if (exists("singlefile_galaxyPaths")){\n+ singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))\n+ singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))\n \n- library(tools)\n+ singlefile=NULL\n+ for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {\n+ singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]\n+ singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]\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+ }\n+ return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))\n+}\n+\n+\n+# This function retrieve the raw file in the working directory\n+# - if zipfile: unzip the file with its directory tree\n+# - if singlefiles: set symlink with the good filename\n+retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {\n+ if(!is.null(singlefile) && (length("singlefile")>0)) {\n+ for (singlefile_sampleName in names(singlefile)) {\n+ singlefile_galaxyPath = singlefile[[singlefile_sampleName]]\n+ if(!file.exists(singlefile_galaxyPath)){\n+ error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")\n+ print(error_message); stop(error_message)\n+ }\n \n- #cat("\\n\\n")\n+ file.symlink(singlefile_galaxyPath,singlefile_sampleName)\n+ }\n+ directory = "."\n+\n+ }\n+ if(!is.null(zipfile) && (zipfile!="")) {\n+ if(!file.exists(zipfile)){\n+ error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")\n+ print(error_message)\n+ stop(error_message)\n+ }\n+\n+ #list all file in the zip file\n+ #zip_files=unzip(zipfile,list=T)[,"Name"]\n \n- return(as.matrix(md5sum(files)))\n+ #unzip\n+ suppressWarnings(unzip(zipfile, unzip="unzip"))\n+\n+ #get the directory name\n+ filesInZip=unzip(zipfile, list=T);\n+ directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));\n+ directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]\n+ directory = "."\n+ if (length(directories) == 1) directory = directories\n+\n+ cat("files_root_directory\\t",directory,"\\n")\n+\n+ }\n+ return (directory)\n }\n' |
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| diff -r 2c1d7df89cf6 -r c81275aee959 macros.xml --- a/macros.xml Mon Jan 30 08:53:13 2017 -0500 +++ b/macros.xml Fri Apr 07 07:35:31 2017 -0400 |
| [ |
| @@ -7,6 +7,11 @@ <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> </xml> + <xml name="requirements_light"> + <requirements> + <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> + </requirements> + </xml> <xml name="stdio"> <stdio> <exit_code range="1" level="fatal" /> @@ -20,41 +25,101 @@ <token name="@COMMAND_LOG_EXIT@"> ; return=\$?; - mv log.txt $log; - cat $log; + mv log.txt '$log'; + cat '$log'; sh -c "exit \$return" </token> <!-- zipfile load for planemo test --> - <token name="@COMMAND_ZIPFILE_LOAD@"> - #if $zipfile_load_conditional.zipfile_load_select == "yes": - #if $zipfile_load_conditional.zip_file: - zipfile $zipfile_load_conditional.zip_file + <token name="@COMMAND_FILE_LOAD@"> + #if $file_load_section.file_load_conditional.file_load_select == "yes": + #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #else + zipfile '$file_load_section.file_load_conditional.input' #end if #end if </token> - <xml name="zipfile_load"> - <conditional name="zipfile_load_conditional"> - <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes">yes</option> - </param> - <when value="no"> + <xml name="input_file_load"> + <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> + <conditional name="file_load_conditional"> + <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" >yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> + </when> + </conditional> + </section> + </xml> + + <xml name="test_file_load_zip"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> + </conditional> + </section> + </xml> + + <xml name="test_file_load_single"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + </conditional> + </section> + </xml> + + <token name="@COMMAND_PEAKLIST@"> + #if $peaklist.peaklistBool + variableMetadataOutput '$variableMetadata' + dataMatrixOutput '$dataMatrix' + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + #end if + </token> + + <xml name="input_peaklist"> + <conditional name="peaklist"> + <param name="peaklistBool" type="boolean" label="Get a Peak List" /> + <when value="true"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> + <option value="into" selected="true">into</option> + <option value="maxo">maxo</option> + <option value="intb">intb</option> + </param> </when> - <when value="yes"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> + <when value="false" /> </conditional> </xml> - + <xml name="output_peaklist" token_function=""> + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv"> + <filter>(peaklist['peaklistBool'])</filter> + </data> + <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" > + <filter>(peaklist['peaklistBool'])</filter> + </data> + </xml> <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 +**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 |
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| diff -r 2c1d7df89cf6 -r c81275aee959 planemo_test.sh --- a/planemo_test.sh Mon Jan 30 08:53:13 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,30 +0,0 @@ -# Example of planemo command to launch test - - -# -- 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-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh -planemo test --install_galaxy - -#All 2 test(s) executed passed. -#abims_xcms_group[0]: passed -#abims_xcms_group[1]: 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 2 test(s) executed passed. -#abims_xcms_group[0]: passed -#abims_xcms_group[1]: passed - - -# -- Use of shed_test -planemo shed_test --install_galaxy -t testtoolshed - -#All 2 test(s) executed passed. -#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.0.5[0]: passed -#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.0.5[1]: passed |
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| b |
| b'@@ -0,0 +1,8276 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|
| b |
| diff -r 2c1d7df89cf6 -r c81275aee959 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 30 08:53:13 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="R" version="3.1.2"> - <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bioconductor-xcms" version="1.46.0"> - <repository changeset_revision="779207ed5674" name="package_bioconductor_xcms_1_46_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r 2c1d7df89cf6 -r c81275aee959 xcms.r --- a/xcms.r Mon Jan 30 08:53:13 2017 -0500 +++ b/xcms.r Fri Apr 07 07:35:31 2017 -0400 |
| [ |
| b'@@ -15,8 +15,8 @@\n #pkgs=c("xcms","batch")\n pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")\n for(pkg in pkgs) {\n- suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))\n- cat(pkg,"\\t",as.character(packageVersion(pkg)),"\\n",sep="")\n+ suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))\n+ cat(pkg,"\\t",as.character(packageVersion(pkg)),"\\n",sep="")\n }\n source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }\n cat("\\n\\n");\n@@ -38,7 +38,7 @@\n \n #image is an .RData file necessary to use xset variable given by previous tools\n if (!is.null(listArguments[["image"]])){\n- load(listArguments[["image"]]); listArguments[["image"]]=NULL\n+ load(listArguments[["image"]]); listArguments[["image"]]=NULL\n }\n \n #Import the different functions\n@@ -61,110 +61,67 @@\n \n xsetRdataOutput = paste(thefunction,"RData",sep=".")\n if (!is.null(listArguments[["xsetRdataOutput"]])){\n- xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL\n+ xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL\n }\n \n #saving the specific parameters\n rplotspdf = "Rplots.pdf"\n if (!is.null(listArguments[["rplotspdf"]])){\n- rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL\n+ rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL\n }\n sampleMetadataOutput = "sampleMetadata.tsv"\n if (!is.null(listArguments[["sampleMetadataOutput"]])){\n- sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL\n+ sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL\n }\n variableMetadataOutput = "variableMetadata.tsv"\n if (!is.null(listArguments[["variableMetadataOutput"]])){\n- variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL\n+ variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL\n }\n dataMatrixOutput = "dataMatrix.tsv"\n if (!is.null(listArguments[["dataMatrixOutput"]])){\n- dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL\n+ dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL\n }\n if (!is.null(listArguments[["convertRTMinute"]])){\n- convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL\n+ convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL\n }\n if (!is.null(listArguments[["numDigitsMZ"]])){\n- numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL\n+ numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL\n }\n if (!is.null(listArguments[["numDigitsRT"]])){\n numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL\n }\n if (!is.null(listArguments[["intval"]])){\n- intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL\n+ intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL\n }\n \n if (thefunction %in% c("xcmsSet","retcor")) {\n- ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL\n- bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL\n-}\n-\n-#necessary to unzip .zip file uploaded to Galaxy\n-#thanks to .zip file it\'s possible to upload many file as the same time conserving the tree hierarchy of directories\n-\n-\n-if (!is.null(listArguments[["zipfile"]])){\n- zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL\n-}\n-\n-if (!is.null(listArguments[["library"]])){\n- directory=listArguments[["library"]]; listArguments[["library"]]'..b'set), listArguments)\n }\n \n cat("\\n\\n")\n@@ -172,8 +129,6 @@\n \n \n \n-\n-\n # ----- MAIN PROCESSING INFO -----\n cat("\\tMAIN PROCESSING INFO\\n")\n \n@@ -181,12 +136,12 @@\n #Verification of a group step before doing the fillpeaks job.\n \n if (thefunction == "fillPeaks") {\n- res=try(is.null(groupnames(xset)))\n- if (class(res) == "try-error"){\n- error<-geterrmessage()\n- write(error, stderr())\n- stop("You must always do a group step after a retcor. Otherwise it won\'t work for the fillpeaks step")\n- }\n+ res=try(is.null(groupnames(xset)))\n+ if (class(res) == "try-error"){\n+ error<-geterrmessage()\n+ write(error, stderr())\n+ stop("You must always do a group step after a retcor. Otherwise it won\'t work for the fillpeaks step")\n+ }\n \n }\n \n@@ -194,7 +149,7 @@\n #dev.new(file="Rplots.pdf", width=16, height=12)\n pdf(file=rplotspdf, width=16, height=12)\n if (thefunction == "group") {\n- par(mfrow=c(2,2))\n+ par(mfrow=c(2,2))\n }\n #else if (thefunction == "retcor") {\n #try to change the legend display\n@@ -208,6 +163,11 @@\n cat("\\t\\tCOMPUTE\\n")\n xset = do.call(thefunction, listArguments)\n \n+# check if there are no peaks\n+if (nrow(peaks(xset)) == 0) {\n+ stop("No peaks were detected. You should review your settings")\n+}\n+\n \n cat("\\n\\n")\n \n@@ -215,40 +175,38 @@\n \n if (thefunction == "xcmsSet") {\n \n- #transform the files absolute pathways into relative pathways\n- xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)\n+ #transform the files absolute pathways into relative pathways\n+ xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)\n+ if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {\n \n- if(exists("zipfile") && (zipfile!="")) {\n+ #Modify the samples names (erase the path)\n+ for(i in 1:length(sampnames(xset))){\n \n- #Modify the samples names (erase the path)\n- for(i in 1:length(sampnames(xset))){\n+ sample_name=unlist(strsplit(sampnames(xset)[i], "/"))\n+ sample_name=sample_name[length(sample_name)]\n+ sample_name= unlist(strsplit(sample_name,"[.]"))[1]\n+ sampnames(xset)[i]=sample_name\n \n- sample_name=unlist(strsplit(sampnames(xset)[i], "/"))\n- sample_name=sample_name[length(sample_name)]\n- sample_name= unlist(strsplit(sample_name,"[.]"))[1]\n- sampnames(xset)[i]=sample_name\n+ }\n \n }\n \n- }\n-\n }\n \n # -- TIC --\n if (thefunction == "xcmsSet") {\n- cat("\\t\\tGET TIC GRAPH\\n")\n- sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)\n- getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")\n- getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)\n+ cat("\\t\\tGET TIC GRAPH\\n")\n+ sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)\n+ getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")\n+ getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)\n } else if (thefunction == "retcor") {\n- cat("\\t\\tGET TIC GRAPH\\n")\n- getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")\n- getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)\n+ cat("\\t\\tGET TIC GRAPH\\n")\n+ getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")\n+ getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)\n }\n \n-if (thefunction == "fillPeaks") {\n- cat("\\t\\tGET THE PEAK LIST\\n")\n- getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)\n+if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {\n+ getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)\n }\n \n \n@@ -262,7 +220,7 @@\n \n \n #saving R data in .Rdata file to save the variables used in the present tool\n-objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList")\n+objects2save = c("xset","zipfile","singlefile","listOFlistArguments","md5sumList","sampleNamesList")\n save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)\n \n cat("\\n\\n")\n' |
