Mercurial > repos > mmonsoor > camera_combinexsannos
changeset 12:ddce949e4b35 draft
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
| author | lecorguille |
|---|---|
| date | Tue, 28 Mar 2017 10:51:55 -0400 |
| parents | d67f7aa847bf |
| children | 97e2c754e81f |
| files | CAMERA.r abims_CAMERA_combinexsAnnos.xml lib.r macros.xml |
| diffstat | 4 files changed, 196 insertions(+), 107 deletions(-) [+] |
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--- a/CAMERA.r Mon Feb 13 11:19:39 2017 -0500 +++ b/CAMERA.r Tue Mar 28 10:51:55 2017 -0400 @@ -98,64 +98,13 @@ #Import the different functions source_local("lib.r") -#necessary to unzip .zip file uploaded to Galaxy -#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories - -if (!is.null(listArguments[["zipfile"]])){ - zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL -} - -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("annotatediff")) { - 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 = "." - - - } - 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") - - } + rawFilePath = getRawfilePathFromArguments(listArguments) + zipfile = rawFilePath$zipfile + singlefile = rawFilePath$singlefile + listArguments = rawFilePath$listArguments + directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) }
--- a/abims_CAMERA_combinexsAnnos.xml Mon Feb 13 11:19:39 2017 -0500 +++ b/abims_CAMERA_combinexsAnnos.xml Tue Mar 28 10:51:55 2017 -0400 @@ -54,10 +54,7 @@ <param name="pos" value="TRUE"/> <param name="tol" value="2"/> <param name="ruleset" value="1,1"/> - <param name="convertRTMinute" value="True"/> - <param name="numDigitsMZ" value="4" /> - <param name="numDigitsRT" value="1" /> - <param name="intval" value="into"/> + <expand macro="test_peaklist"/> <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> </test> </tests>
--- a/lib.r Mon Feb 13 11:19:39 2017 -0500 +++ b/lib.r Tue Mar 28 10:51:55 2017 -0400 @@ -223,3 +223,84 @@ return(variableMetadata); } + +# 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 Mon Feb 13 11:19:39 2017 -0500 +++ b/macros.xml Tue Mar 28 10:51:55 2017 -0400 @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="0.4_1">r-snow</requirement> <requirement type="package" version="1.26.0">bioconductor-camera</requirement> <requirement type="package" version="2.26.0">bioconductor-multtest</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="1.6.27">libpng</requirement> - <requirement type="package" version="1.3.20">graphicsmagick</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.3.23">graphicsmagick</requirement> </requirements> </xml> <xml name="stdio"> @@ -20,61 +19,124 @@ LANG=C Rscript $__tool_directory__/CAMERA.r </token> - <!-- zipfile load for planemo test --> + <!-- raw file 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' + #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 - #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 $file_load_conditional.inputs.single_file ] ) - - singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + zipfile '$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> + + <!-- peaklist export option management --> <token name="@COMMAND_PEAKLIST@"> - convertRTMinute $convertRTMinute - numDigitsMZ $numDigitsMZ - numDigitsRT $numDigitsRT - intval $intval + convertRTMinute $export.convertRTMinute + numDigitsMZ $export.numDigitsMZ + numDigitsRT $export.numDigitsRT + intval $export.intval </token> <xml name="input_peaklist"> - <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="General used intensity value" 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> + <section name="export" title="Export options"> + <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="General used intensity value" 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> + </section> + </xml> + + <xml name="test_peaklist"> + <section name="export"> + <param name="convertRTMinute" value="True"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + <param name="intval" value="into"/> + </section> + </xml> + + <!-- annotate_diffreport <test> commun part --> + <xml name="test_annotate_diffreport"> + <section name="groupfwhm"> + <param name="sigma" value="6"/> + <param name="perfwhm" value="0.6"/> + </section> + <section name="findisotopes"> + <param name="maxcharge" value="3"/> + <param name="maxiso" value="4"/> + <param name="minfrac" value="0.5"/> + </section> + <section name="general"> + <param name="ppm" value="5"/> + <param name="mzabs" value="0.015"/> + <param name="max_peaks" value="100"/> + </section> + <section name="diffreport"> + <conditional name="options"> + <param name="option" value="show"/> + <param name="eicmax" value="200"/> + <param name="eicwidth" value="200"/> + <param name="value" value="into"/> + <param name="h" value="480"/> + <param name="w" value="640"/> + <param name="mzdec" value="2"/> + <param name="sortpval" value="False"/> + </conditional> + </section> + <expand macro="test_peaklist"/> + </xml> + + <xml name="test_annotate_diffreport_quick"> + <param name="quick" value="FALSE"/> + <section name="groupcorr"> + <param name="cor_eic_th" value="0.75"/> + <param name="graphMethod" value="hcs"/> + <param name="pval" value="0.05"/> + <param name="calcCiS" value="True"/> + <param name="calcIso" value="False"/> + <param name="calcCaS" value="False"/> + </section> </xml> <token name="@HELP_AUTHORS@">