Mercurial > repos > lecorguille > xcms_xcmsset
changeset 24:d8915395681f draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
| author | lecorguille |
|---|---|
| date | Wed, 01 Mar 2017 16:56:01 -0500 |
| parents | 329cfa3d2be6 |
| children | dc4d3e2b9968 |
| files | abims_xcms_xcmsSet.xml lib.r macros.xml xcms.r |
| diffstat | 4 files changed, 146 insertions(+), 122 deletions(-) [+] |
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--- a/abims_xcms_xcmsSet.xml Fri Feb 10 11:01:21 2017 -0500 +++ b/abims_xcms_xcmsSet.xml Wed Mar 01 16:56:01 2017 -0500 @@ -11,10 +11,10 @@ <command><![CDATA[ @COMMAND_XCMS_SCRIPT@ - #if $inputs.input == "zip_file": - zipfile '$inputs.zip_file' - #elif $inputs.input == "single_file": - singlefile_galaxyPath '$inputs.single_file' singlefile_sampleName '$inputs.single_file.name' + #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): + singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' + #else + zipfile '$input' #end if xfunction xcmsSet @@ -65,18 +65,7 @@ <inputs> - <conditional name="inputs"> - <param name="input" type="select" label="Choose your inputs method" > - <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> - <option value="single_file">mzXML file from your history</option> - </param> - <when value="zip_file"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - <when value="single_file"> - <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" /> - </when> - </conditional> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" 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." /> <conditional name="options_scanrange"> <param name="option" type="select" label="Scan range option " > @@ -221,8 +210,7 @@ </output> </test>--> <test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="25" /> <param name="methods|peakwidth" value="20,50" /> @@ -307,8 +295,7 @@ </output> </test>--> <test> - <param name="inputs|input" value="single_file" /> - <param name="inputs|single_file" value="HU_neg_017.mzXML" ftype="mzxml" /> + <param name="input" value="HU_neg_017.mzXML" ftype="mzxml" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="25" /> <param name="methods|peakwidth" value="20,50" /> @@ -324,8 +311,7 @@ </output> </test> <test> - <param name="inputs|input" value="single_file" /> - <param name="inputs|single_file" value="MM14.mzML" ftype="mzxml" /> + <param name="input" value="MM14.mzML" ftype="mzxml" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="56" /> <param name="methods|peakwidth" value="5.275,13.5" /> @@ -405,20 +391,20 @@ Input files ----------- -+---------------------------+--------------------+ -| Parameter : num + label | Format | -+===========================+====================+ -| OR : Zip file | zip | -+---------------------------+--------------------+ -| OR : Single file | mzXML, netCDF | -+---------------------------+--------------------+ ++---------------------------+----------------------------------+ +| Parameter : num + label | Format | ++===========================+==================================+ +| OR : Zip file | zip | ++---------------------------+----------------------------------+ +| OR : Single file | mzXML, mzML, mzData, netCDF | ++---------------------------+----------------------------------+ **Choose your inputs** You have two methods for your inputs: - | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). - | Single file: You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group" + | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group" + | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). Zip file: Steps for creating the zip file -----------------------------------------
--- a/lib.r Fri Feb 10 11:01:21 2017 -0500 +++ b/lib.r Wed Mar 01 16:56:01 2017 -0500 @@ -473,3 +473,85 @@ return(as.matrix(md5sum(files))) } + + +# This function get the raw file path from the arguments +getRawfilePathFromArguments <- function(listArguments) { + zipfile = NULL + singlefile = NULL + if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]] + if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]] + if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]] + + if (!is.null(listArguments[["singlefile_galaxyPath"]])) { + singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]]; + singlefile_sampleNames = listArguments[["singlefile_sampleName"]] + } + if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) { + singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]]; + singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]] + } + if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) { + singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]]; + singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]] + } + if (exists("singlefile_galaxyPaths")){ + singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,",")) + singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,",")) + + singlefile=NULL + for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { + singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i] + singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i] + singlefile[[singlefile_sampleName]] = singlefile_galaxyPath + } + } + for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { + listArguments[[argument]]=NULL + } + return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments)) +} + + +# This function retrieve the raw file in the working directory +# - if zipfile: unzip the file with its directory tree +# - if singlefiles: set symlink with the good filename +retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { + if(!is.null(singlefile) && (length("singlefile")>0)) { + for (singlefile_sampleName in names(singlefile)) { + singlefile_galaxyPath = singlefile[[singlefile_sampleName]] + if(!file.exists(singlefile_galaxyPath)){ + error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") + print(error_message); stop(error_message) + } + + file.symlink(singlefile_galaxyPath,singlefile_sampleName) + } + directory = "." + + } + if(!is.null(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") + + } + return (directory) +}
--- a/macros.xml Fri Feb 10 11:01:21 2017 -0500 +++ b/macros.xml Wed Mar 01 16:56:01 2017 -0500 @@ -33,41 +33,50 @@ <!-- zipfile load for planemo test --> <token name="@COMMAND_FILE_LOAD@"> - #if $file_load_conditional.file_load_select == "yes": - #if $file_load_conditional.inputs.input == "zip_file": - zipfile '$file_load_conditional.inputs.zip_file' - #else - #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] ) - #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] ) + #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="file_load"> - <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"> - <conditional name="inputs"> - <param name="input" type="select" label="Choose your inputs method" > - <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> - <option value="single_file">A mzXML or netCDF file from your history</option> - </param> - <when value="zip_file"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - <when value="single_file"> - <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/> - </when> - </conditional> - </when> - </conditional> + <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@">
--- a/xcms.r Fri Feb 10 11:01:21 2017 -0500 +++ b/xcms.r Wed Mar 01 16:56:01 2017 -0500 @@ -71,7 +71,7 @@ } sampleMetadataOutput = "sampleMetadata.tsv" if (!is.null(listArguments[["sampleMetadataOutput"]])){ - sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL + sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL } variableMetadataOutput = "variableMetadata.tsv" if (!is.null(listArguments[["variableMetadataOutput"]])){ @@ -99,67 +99,14 @@ 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[["singlefile_galaxyPath"]])){ - singlefile_galaxyPaths = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL - singlefile_sampleNames = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL - - singlefile=NULL - for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { - singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i] - singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i] - singlefile[[singlefile_sampleName]] = singlefile_galaxyPath - } -} - -# We unzip automatically the chromatograms from the zip files. if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { - if(exists("singlefile") && (length("singlefile")>0)) { - for (singlefile_sampleName in names(singlefile)) { - singlefile_galaxyPath = singlefile[[singlefile_sampleName]] - if(!file.exists(singlefile_galaxyPath)){ - error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") - print(error_message); stop(error_message) - } - - file.symlink(singlefile_galaxyPath,singlefile_sampleName) - } - directory = "." - - md5sumList=list("origin"=getMd5sum(directory)) - - } - 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)) - } + rawFilePath = getRawfilePathFromArguments(listArguments) + zipfile = rawFilePath$zipfile + singlefile = rawFilePath$singlefile + listArguments = rawFilePath$listArguments + directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) + md5sumList=list("origin"=getMd5sum(directory)) } #addition of the directory to the list of arguments in the first position @@ -223,8 +170,8 @@ #transform the files absolute pathways into relative pathways xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) - - if(exists("zipfile") && (zipfile!="")) { + print(zipfile) + if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) { #Modify the samples names (erase the path) for(i in 1:length(sampnames(xset))){