| Previous changeset 2:3a9914b37f2f (2016-07-04) Next changeset 4:52b222a626b0 (2017-04-07) |
|
Commit message:
planemo upload commit c897279aa8cae0a4ad889bb05b143f32d2b6d712 |
|
modified:
ProbMetab.xml README.txt lib.r macros.xml probmetab.r static/images/probmetab_workflow.png |
|
added:
test-data/faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata test-data/ko15.CDF test-data/ko16.CDF test-data/wt15.CDF test-data/wt16.CDF |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 ProbMetab.xml --- a/ProbMetab.xml Mon Jul 04 11:58:10 2016 -0400 +++ b/ProbMetab.xml Fri Apr 07 07:14:12 2017 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="Probmetab" name="ProbMetab Tool" version="1.0.1">\n+<tool id="Probmetab" name="ProbMetab Tool" version="1.1.0">\n \n <description>Wrapper function for ProbMetab R package.</description>\n \n@@ -12,201 +12,243 @@\n <command>\n @COMMAND_CAMERA_SCRIPT@\n #if $acquisition_options.mode == "one":\n- mode_acquisition $acquisition_options.mode xa $acquisition_options.xa\n+ mode_acquisition $acquisition_options.mode\n+ image \'$acquisition_options.image\'\n ##if $acquisition_options.xsetnofill_options.option == "show":\n-\t ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill\n- \t ##end if\t\n+ ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill\n+ ##end if\n+\n+ @COMMAND_FILE_LOAD_ONE@\n+\n #else\n- mode_acquisition $acquisition_options.mode inputs_mode $acquisition_options.input_mode.option\n+ mode_acquisition $acquisition_options.mode\n+ inputs_mode $acquisition_options.input_mode.option\n #if $acquisition_options.input_mode.option== "two":\n \n-\t image_pos $acquisition_options.input_mode.image_pos image_neg $acquisition_options.input_mode.image_neg\n-\t ##if $acquisition_options.input_mode.xsetnofill_options.option == "show":\n-\t\t ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill\n- \t\t##end if\t\t\n+ image_pos \'$acquisition_options.input_mode.image_pos\'\n+ image_neg \'$acquisition_options.input_mode.image_neg\'\n+ ##if $acquisition_options.input_mode.xsetnofill_options.option == "show":\n+ ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill\n+ ##xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill\n+ ##end if\n+\n+ @COMMAND_FILE_LOAD_POSITIVE@\n+ @COMMAND_FILE_LOAD_NEGATIVE@\n ##else\n-\t ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos image_pos $acquisition_options.input_mode.image_pos\n+ ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos\n+ ##image_pos $acquisition_options.input_mode.image_pos\n #end if\n \n #end if\n \n- #if $option_toexclude.option == "show":\n- \ttoexclude $option_toexclude.toexclude\n+ ## Extraction of CAMERA annotation [get.annot]\n+ allowMiss $getannot.allowMiss\n+ #if $getannot.option_toexclude.option == "show":\n+ toexclude $getannot.option_toexclude.toexclude\n #end if\n- allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol\n- opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob\n- \n- @COMMAND_ZIPFILE_LOAD@\n+\n+ ## Database matching [create.reactionM]\n+ kegg_db $db.kegg_db\n+ ppm_tol $db.ppm_tol\n+\n+ ## Probability calculations matrix export [export.class.table]\n+ prob $export.prob\n+ html $export.html\n+\n+ ## Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor]\n+ opt $reac2cor.opt\n+ corprob $reac2cor.corprob\n+ pcorprob $reac2cor.pcorprob\n+ corths $reac2cor.corths\n+\n+ @COMMAND_LOG_EXIT@\n \n </command>\n \n <inputs>\n \n <conditional name="acquisition_options">\n-\t <param name="mode" type="select" label="Choose your acquisition mode" >\n-\t\t <option value="one" selected="true" >One acquisition charge mode</option>\n- \t<option value="two" >Two acquisition charge mode (positif and negatif)</option>\n-\t </param>\n-\n-\t <!-- One acquisition mode-->\n-\t <when value="one">\n-\t\t <param name="xa" type="data" label="Annotate RD'..b'>\n+ <expand macro="test_commun"/>\n+ <expand macro="test_file_load_zip"/>\n+ <assert_stdout>\n+ <has_text text="Step 1... determine cutoff point" />\n+ <has_text text="Step 2... estimate parameters of null distribution and eta0" />\n+ <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" />\n+ <has_text text="Step 4... compute q-values and local fdr" />\n+ </assert_stdout>\n+ </test>\n+ <test>\n+ <conditional name="acquisition_options">\n+ <param name="mode" value="one" />\n+ <param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" />\n+ </conditional>\n+ <expand macro="test_commun"/>\n+ <expand macro="test_file_load_single"/>\n+ <assert_stdout>\n+ <has_text text="Step 1... determine cutoff point" />\n+ <has_text text="Step 2... estimate parameters of null distribution and eta0" />\n+ <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" />\n+ <has_text text="Step 4... compute q-values and local fdr" />\n+ </assert_stdout>\n </test>\n </tests>\n \n \n <help>\n-\t\n+\n @HELP_AUTHORS@\n \n =========\n@@ -225,7 +267,7 @@\n **Details**\n \n ProbMetab assumes peak detection, retention time correction and peak grouping [4, 5] in order to\n-perform mass peak to compound assignment. \n+perform mass peak to compound assignment.\n \n Once the initial annotation for different forms of the same ion (adducts and isotopes), is defined,\n one can seek for a non-redundant set of putative molecules (after charge and possible adduct\n@@ -235,7 +277,7 @@\n experimental condition. In order to address this issue, a flexible workflow, which allows users to\n integrate different methods, would improve true molecular ions recovery.\n \n-The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data. \n+The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data.\n \n \n \n@@ -250,9 +292,9 @@\n ========================= ========================================== ======= ==========\n Name Output file Format Parameter\n ========================= ========================================== ======= ==========\n-xcms.annotate xset.annotate_POS (or NEG).RData RData RData file \t\t\t\n+xcms.annotate xset.annotate_POS (or NEG).RData RData RData file\n ========================= ========================================== ======= ==========\n- \n+\n \n **General schema of the metabolomic workflow**\n \n@@ -295,7 +337,7 @@\n \n **Calculate**\n \n-**intervals** \n+**intervals**\n A vector of SNR numerical intervals, to which different carbon offset should be added to predicted C-number.\n \n **offset**\n@@ -309,7 +351,7 @@\n \n Which noise model to use, "erfc" to complementary error function, or "gaussian" to standard gaussian with two sd corresponding to the given p.p.m precision.\n \n-**precision** \n+**precision**\n \n Equipment mass accuracy, usually the same used in exact mass search.\n \n@@ -384,6 +426,12 @@\n Changelog/News\n --------------\n \n+**Version 1.1.0 - 06/04/2017**\n+\n+- IMPROVEMENT: add some sections within to separate the different parts of the process\n+\n+- IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet\n+\n **Version 1.0.1 - 16/05/2016**\n \n - TEST: refactoring to pass planemo test using conda dependencies\n@@ -393,10 +441,8 @@\n \n - NEW: ProbMetab first version\n \n- \n+\n </help>\n \n <expand macro="citation" />\n </tool>\n- \n- \n' |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 README.txt --- a/README.txt Mon Jul 04 11:58:10 2016 -0400 +++ b/README.txt Fri Apr 07 07:14:12 2017 -0400 |
| b |
| @@ -1,19 +1,17 @@ Changelog/News -------------- +**Version 1.1.0 - 06/04/2017** + +- IMPROVEMENT: add some sections within to separate the different parts of the process + +- IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet + **Version 1.0.1 - 16/05/2016** - TEST: refactoring to pass planemo test using conda dependencies - **Version 1.0.0 - 10/06/2015** - NEW: ProbMetab first version - -Test Status ------------ - -Planemo test using conda: passed - -Planemo shed_test : passed |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 lib.r --- a/lib.r Mon Jul 04 11:58:10 2016 -0400 +++ b/lib.r Fri Apr 07 07:14:12 2017 -0400 |
| [ |
| b'@@ -1,323 +1,400 @@\n-# lib.r ProbMetab version="1.0.0"\r\n-# Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr\r\n-# Contributors: Yann Guitton and Jean-francois Martin\r\n-\r\n-\r\n-##Main probmetab function launch by the Galaxy ProbMetab wrapper\r\n-probmetab = function(xa, xaP, xaN, variableMetadata, variableMetadataP, variableMetadataN, listArguments){\r\n-\t##ONE MODE ACQUISITION##\r\n-\tif(listArguments[["mode_acquisition"]]=="one") {\r\n-\t\tcomb=NULL\n-\r\n-\t\t#Get the polarity from xa object\r\n-\t\tpolarity=xa@polarity\r\n-\t\t#SNR option\r\n-\t\tif ("xsetnofill" %in% names(listArguments)) {\r\n-\t\t\tload(listArguments[["xsetnofill"]])\r\n-\t\t\txsetnofill=xset\r\n-\t\t}\r\n-\t\telse{\r\n-\t\t\txsetnofill=NULL\r\n-\t\t}\r\n-\t\t#Exclude samples\r\n-\t\tif ("toexclude" %in% names(listArguments)) {\r\n-\t\t\ttoexclude=listArguments[["toexclude"]]\r\n-\t\t}\r\n-\t\telse {\r\n-\t\t\ttoexclude=NULL\r\n-\t\t}\r\n-\t\tionAnnot=get.annot(xa, polarity=polarity, allowMiss=listArguments[["allowMiss"]],xset=xsetnofill,toexclude=toexclude)\r\n-\t\tcomb=NULL\r\n-\t}\r\n-\r\n-\t##TWO MODES ACQUISITION##\r\n-\t#Mode annotatediffreport\r\n-\telse if(listArguments[["inputs_mode"]]=="two"){\r\n-\t\t##Prepare the objects that will be used for the get.annot function\r\n-\t\tcomb=1\r\n-\t\t\r\n-\r\n-\t\txsetPnofill=NULL\r\n-\t\txsetNnofill=NULL\r\n-\t\t# TODO: a reactiver\t\t\n-\t\t#if ("xsetPnofill" %in% names(listArguments)) {\r\n-\t\t#\tload(listArguments[["xsetPnofill"]])\r\n-\t\t#\txsetPnofill=xset\r\n-\t\t#}\r\n-\t\t#if ("xsetNnofill" %in% names(listArguments)) {\r\n-\t\t#\tload(listArguments[["xsetNnofill"]])\r\n-\t\t#\txsetNnofill=xset\r\n-\t\t#}\r\n-\t\t# include CAMERA non-annotated compounds, and snr retrieval \r\n-\t\t# comb 2+ - used on Table 1\t\r\n-\t\tionAnnotP2plus = get.annot(axP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]]) \r\n-\t\tionAnnotN2plus = get.annot(axN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]])\r\n-\t\tionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus)\r\n-\t\tprint(sum(ionAnnot$molIon[,3]==1))\r\n-\t\tprint(sum(ionAnnot$molIon[,3]==0))\r\n-\t\twrite.table(ionAnnot[1], sep="\\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv")\r\n-\t\t#Merge variableMetadata Negative and positive acquisitions mode\r\n-\t\t\r\n-\r\n-\t\t#Mode combinexsannos TODO bug avec tableau issus de combinexsannos\r\n-\t\t#else {\r\n-\t\t\t#load(listArguments[["image_combinexsannos"]])\r\n-\t\t\t#image_combinexsannos=cAnnot\r\n-\t\t\t##Prepare the objects that will be used for the combineMolIon function\r\n-\t\t\t#load(listArguments[["image_pos"]])\r\n-\t\t\t#image_pos=xa\r\n-\t\t\t#ionAnnot=combineMolIon(peaklist=cAnnot, cameraobj=image_pos, polarity="pos")\r\n-\t\t#}\r\n-\t\t\r\n-\t}\r\n-\r\n-\t##DATABASE MATCHING##\r\n-\tif (listArguments[["kegg_db"]]=="KEGG"){\t\t\r\n-\t\tDB=build.database.kegg(orgID = NULL)\r\n-\t}\r\n-\telse{\t\r\n-\t\ttable_list <<- NULL\r\n-\t\tids=strsplit(listArguments[["kegg_db"]],",")\r\n-\t\tids=ids[[1]]\r\n-\t\tif(length(ids)>1){\r\n-\t\t\tfor(i in 1:length(ids)){\r\n-\t\t\t\t table_list[[i]] <- build.database.kegg(ids[i])\r\n-\t\t\t}\r\n-\t\t\tdb_table=do.call("rbind",table_list)\r\n-\t\t\tDB=unique(db_table)\r\n-\t\t}\r\n-\t\telse{\r\n-\t\t\tDB=build.database.kegg(listArguments[["kegg_db"]])\r\n-\t\t}\r\n-\t}\t\r\n-\t#Matching des mass exactes mesurees avec les masses des compounds KEGG (pas M+H ou M-H)\r\n-\treactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]])\r\n-\t##PROBABILITY RANKING##\r\n-\t# number of masses with candidates inside the fixed mass window\r\n-\t# and masses with more than one candidate\r\n-\tlength(unique(reactionM[reactionM[,"id"]!="unknown",1])) \r\n-\tsum(table(reactionM[reactionM[,"id"]!="unknown",1])>1)\r\n-\t#if (listArguments[["useIso"]]){\r\n-\t\t#BUG TODO\r\n-\t\t# Calculate the ratio between observed and theoretical isotopic patterns.\r\n-\t\t# If you don\'t have an assessment of carbon offset to carbon number prediction \r\n-\t\t# skip this step and use the reactionM as input to weigthM function. \r\n-\t\t#isoPatt < incorporate.isotopes(comb2plus, reactionM, , samp=12:23, DB=DB) \r\n-\t\t# calculate the likelihood of each mass to compound assignment using mass accuracy,and i'..b'ariableMetadata$name= paste("M",round(variableMetadata$mz),"T",round(variableMetadata$rt),sep="")\n-\treturn (variableMetadata)\n-}\r\n+ # --- variableMetadata ---\n+ peakList=getPeaklist(xa)\n+ peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");\n+ variableMetadata=peakList[,!(colnames(peakList) %in% c(sampnames(xa@xcmsSet)))]\n+ variableMetadata$name= groupnames(xa@xcmsSet)\n+ return (variableMetadata)\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+ 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+ return(list(zipfile=zipfile, singlefile=singlefile))\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+\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+ 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+ #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+}\n' |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 macros.xml --- a/macros.xml Mon Jul 04 11:58:10 2016 -0400 +++ b/macros.xml Fri Apr 07 07:14:12 2017 -0400 |
| [ |
| @@ -16,29 +16,102 @@ <token name="@COMMAND_CAMERA_SCRIPT@"> LANG=C Rscript $__tool_directory__/probmetab.r </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_LOG_EXIT@"> + ; + return=\$?; + cat 'log.txt'; + sh -c "exit \$return" + </token> + + <!-- raw file load for planemo test --> + <token name="@COMMAND_FILE_LOAD_NEUTRAL@"> + #if $file_load_section_selected.file_load_conditional.file_load_select == "yes": + #if $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.input ] ) + singlefile_galaxyPath$polarity '$singlefile_galaxyPath' singlefile_sampleName$polarity '$singlefile_sampleName' + #else + zipfile$polarity '$file_load_section_selected.file_load_conditional.input' #end if - #end if + #end if + </token> + + <token name="@COMMAND_FILE_LOAD_ONE@"> + #set file_load_section_selected = $acquisition_options.file_load_section + #set polarity="" + @COMMAND_FILE_LOAD_NEUTRAL@ + </token> + + <token name="@COMMAND_FILE_LOAD_POSITIVE@"> + #set file_load_section_selected = $acquisition_options.file_load_sectionPositive + #set polarity="Positive" + @COMMAND_FILE_LOAD_NEUTRAL@ + </token> + + <token name="@COMMAND_FILE_LOAD_NEGATIVE@"> + #set file_load_section_selected = $acquisition_options.file_load_sectionNegative + #set polarity="Negative" + @COMMAND_FILE_LOAD_NEUTRAL@ </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" selected="peakgroups">yes</option> - </param> - <when value="no"> - </when> - <when value="yes"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - </conditional> + + <xml name="input_file_load" token_polarity=""> + <section name="file_load_section@POLARITY@" title="@POLARITY@ Resubmit your raw dataset or your zip file"> + <conditional name="file_load_conditional"> + <param name="file_load_select" type="select" label="@POLARITY@ 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_commun"> + <section name="getannot"> + <param name="allowMiss" value="TRUE" /> + <conditional name="option_toexclude"> + <param name="option" value="hide" /> + </conditional> + </section> + <section name="db"> + <param name="kegg_db" value="KEGG" /> + <param name="ppm_tol" value="8" /> + </section> + <section name="export"> + <param name="prob" value="count" /> + <param name="html" value="FALSE" /> + </section> + <section name="reac2cor"> + <param name="opt" value="cor" /> + <param name="corprob" value="0.8" /> + <param name="pcorprob" value="0.8" /> + <param name="corths" value="0.75" /> + </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" token_polarity="">> + <section name="file_load_section@POLARITY@"> + <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="@HELP_AUTHORS@"> .. class:: infomark @@ -49,7 +122,7 @@ .. class:: infomark -**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff. +**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr (and Gildas Le Corguillé) from ABIMS TEAM, Station biologique de Roscoff. | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 probmetab.r --- a/probmetab.r Mon Jul 04 11:58:10 2016 -0400 +++ b/probmetab.r Fri Apr 07 07:14:12 2017 -0400 |
| [ |
| @@ -4,7 +4,7 @@ # ----- LOG ----- -log_file=file("probmetab.log", open = "wt") +log_file=file("log.txt", open = "wt") sink(log_file) sink(log_file, type = "out") @@ -12,8 +12,8 @@ cat("\tPACKAGE INFO\n") pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab") for(p in pkgs) { - suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) - cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") + suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) + cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") } source_local <- function(fname){ @@ -21,9 +21,14 @@ base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) source(paste(base_dir, fname, sep="/")) } + +options(bitmapType='cairo') + cat("\n\n") + + # ----- ARGUMENTS ----- -cat("\tARGUMENTS INFO\n") +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') @@ -35,68 +40,59 @@ # ----- INFILE PROCESSING ----- if(listArguments[["mode_acquisition"]]=="one") { - load(listArguments[["xa"]]) - - if (!is.null(listArguments[["zipfile"]])){ - zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL - } - - #Unzip the chromatograms file for plotting EIC pour the HTML file - if(exists("zipfile")) - { - if (zipfile!=""){ - directory=unzip(zipfile) - } - } - if (!exists("xa")) { - xa=xsAnnotate_object - } - source_local("lib.r") - if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa); - + load(listArguments[["image"]]) + cat("\t\tXA OBJECT INFO\n") + print(xa) + + source_local("lib.r") + if (!exists("zipfile")) zipfile=NULL + if (!exists("singlefile")) singlefile=NULL + rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) + zipfile = rawFilePath$zipfile + singlefile = rawFilePath$singlefile + retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) + + if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa); + } else if(listArguments[["inputs_mode"]]=="two"){ - load(listArguments[["image_pos"]]) - - if (!is.null(listArguments[["zipfile"]])){ - zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL - } - - #Unzip the chromatograms file for plotting EIC pour the HTML file - if(exists("zipfile")) { - if (zipfile!=""){ - directory=unzip(zipfile) - } - } - if (!exists("xa")) { - xa=xsAnnotate_object - } - xaP=xa - source_local("lib.r") - if (!exists("variableMetadata")) variableMetadataP= getVariableMetadata(xa) - else variableMetadataP=variableMetadata + + # POSITIVE + load(listArguments[["image_pos"]]) + if (!exists("xa")) xaP=xsAnnotate_object + else xaP=xa + cat("\t\tXA-POSITIVE OBJECT INFO\n") + print(xaP) + + if (!exists("variableMetadata")) variableMetadataP = getVariableMetadata(xa) + else variableMetadataP = variableMetadata - load(listArguments[["image_neg"]]) - - if (!is.null(listArguments[["zipfile"]])){ - zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL - } - - #Unzip the chromatograms file for plotting EIC pour the HTML file - if(exists("zipfile")) { - - if (zipfile!=""){ - directory=unzip(zipfile) - } - } - if (!exists("xa")) { - xa=xsAnnotate_object - } - xaN=xa - source_local("lib.r") - - if (!exists("variableMetadata")) variableMetadataN= getVariableMetadata(xa) - else variableMetadataN=variableMetadata + source_local("lib.r") + if (!exists("zipfile")) zipfile=NULL + if (!exists("singlefile")) singlefile=NULL + rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) + zipfilePos = rawFilePath$zipfile + singlefilePos = rawFilePath$singlefile + retrieveRawfileInTheWorkingDirectory(singlefilePos, zipfilePos) + + # NEGATIVE + load(listArguments[["image_neg"]]) + + if (!exists("xa")) xaN=xsAnnotate_object + else xaN=xa + cat("\t\tXA-NEGATIVE OBJECT INFO\n") + print(xaP) + + if (!exists("variableMetadata")) variableMetadataN = getVariableMetadata(xa) + else variableMetadataN = variableMetadata + + source_local("lib.r") + if (!exists("zipfile")) zipfile=NULL + if (!exists("singlefile")) singlefile=NULL + rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) + zipfileNeg = rawFilePath$zipfile + singlefileNeg = rawFilePath$singlefile + retrieveRawfileInTheWorkingDirectory(singlefileNeg, zipfileNeg) } #Import the different functions @@ -107,13 +103,12 @@ cat("\tMAIN PROCESSING INFO\n") if(listArguments[["mode_acquisition"]]=="one") { - results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments) + results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments) } else if(listArguments[["inputs_mode"]]=="two"){ - results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments) + results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments) } #delete the parameters to avoid the passage to the next tool in .RData image #rm(listArguments) cat("\tDONE\n") #saving R data in .Rdata file to save the variables used in the present tool #save.image(paste("probmetab","RData",sep=".")) - |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 static/images/probmetab_workflow.png |
| b |
| Binary file static/images/probmetab_workflow.png has changed |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 test-data/faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata |
| b |
| Binary file test-data/faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata has changed |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 test-data/ko15.CDF |
| b |
| Binary file test-data/ko15.CDF has changed |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 test-data/ko16.CDF |
| b |
| Binary file test-data/ko16.CDF has changed |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 test-data/wt15.CDF |
| b |
| Binary file test-data/wt15.CDF has changed |
| b |
| diff -r 3a9914b37f2f -r abcfa1648b66 test-data/wt16.CDF |
| b |
| Binary file test-data/wt16.CDF has changed |
