| Next changeset 1:301d7adf862e (2016-07-04) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c |
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MANUAL_INSTALL.txt NmrBucketing_script.R NmrBucketing_wrapper.R NmrBucketing_xml.xml README.rst planemo_test.sh repository_dependencies.xml static/images/MTH - Architecture repertoire Bruker.png static/images/Mth_Travaux.png test-data/MTBLS1.zip test-data/MTBLS1_bucketedData.tabular test-data/MTBLS1_sampleMetadata.tabular test-data/MTBLS1_variableMetadata.tabular tool_dependencies.xml |
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| diff -r 000000000000 -r a99a6026c972 MANUAL_INSTALL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MANUAL_INSTALL.txt Fri Apr 08 10:56:14 2016 -0400 |
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| @@ -0,0 +1,59 @@ +Instructions to integrate the "NMR bucketing" tool into a local instance of Galaxy +Version February 2015 M Tremblay-Franco + + +## --- R bin and Packages : --- ## +R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" +Platform: x86_64-redhat-linux-gnu (64-bit) + +Install the "batch" library, necessary for parseCommandArgs function and the "pracma" library, nessecary for cumtrapz function: + - Download package source (*.tar.gz file) from your favorite CRAN (http://www.r-project.org/) +For example: http://cran.univ-lyon1.fr/ + + - Install package in your R session +install.packages("path/package_name.tar.gz",lib="path",repos=NULL) +For Example: install.packages("/usr/lib64/R/library/pracma_1.8.3.tar",lib="/usr/lib64/R/library",repos=NULL) + + - Finally, load the package into your R session +library(batch) +library(pracma) + + +## --- Config : --- ## + - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add +<section id="id_name" name="Name"> + <tool file="path/NmrBucketing_xml.xml" /> +</section> +to create a new section containing the NMR_Bucketing tool +or add + <tool file="path/NmrBucketing_xml.xml" /> +in an existing section + + - Put the three files NmrBucketing_xml.xml, NmrBucketing_wrapper.R and NmrBucketing_script.R in a same directory +For example, path=/galaxy/dist/galaxy-dist/tools/stats + + - Edit the NmrBucketing_xml.xml file and change the path in the following lines + # R script + R --vanilla --slave --no-site-file --file=path/NmrBucketing_wrapper.R --args + + ## Library name for raw files storage + library path/$library + +## --- XML help part --- ## +one image: +Copy the 'Mth_Architecture_Repertoire_Bruker.png' file within the directory to your galaxy-dist/static/images/ + + + - Activate the "user_library_import_dir" in your /galaxy/dist/galaxy-dist/universe_wsgi.ini and create the users directories in this path, for example: + + #In universe_wsgi.ini + user_library_import_dir = /projet/sbr/galaxy/import/user + + #Create the user "myaccount" in this path + + User path: /projet/sbr/galaxy/import/user/myaccount@sb-roscoff.fr + + + + +Finally, restart Galaxy \ No newline at end of file |
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| diff -r 000000000000 -r a99a6026c972 NmrBucketing_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrBucketing_script.R Fri Apr 08 10:56:14 2016 -0400 |
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| b'@@ -0,0 +1,245 @@\n+################################################################################################\r\n+# SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES #\r\n+# User : Galaxy #\r\n+# Original data : -- #\r\n+# Starting date : 20-10-2014 #\r\n+# Version 1 : 18-12-2014 #\r\n+# Version 2 : 07-01-2015 #\r\n+# #\r\n+# Input files : files in included in user-defined directory #\r\n+################################################################################################\r\n+NmrBucketing <- function(directory,leftBorder = 10.0,rightBorder = 0.5,bucketSize = 0.04,exclusionZones,exclusionZonesBorders=NULL,\r\n+ graph=c("None","Overlay","One_per_individual"),nomFichier,savLog.txtC = NULL) \r\n+{\r\n+ ## Option\r\n+ ##---------------\r\n+ strAsFacL <- options()$stringsAsFactors\r\n+ options(stingsAsFactors = FALSE)\r\n+ options(warn = -1)\r\n+ \r\n+ \r\n+ ## Constants\r\n+ ##---------------\r\n+ topEnvC <- environment()\r\n+ flgC <- "\\n"\r\n+ \r\n+ ## Log file (in case of integration into Galaxy)\r\n+ ##----------------------------------------------\r\n+ if(!is.null(savLog.txtC))\r\n+ sink(savLog.txtC, append = TRUE)\r\n+ \r\n+ ## Functions definition\r\n+ ##--------------------- \r\n+ ## RAW BRUKER FILE READING FUNCTION\r\n+ NmRBrucker_read <- function(DataDir,SampleSpectrum)\r\n+ {\r\n+ \r\n+ bruker.get_param <- function (ACQ,paramStr)\r\n+ {\r\n+ regexpStr <- paste("^...",paramStr,"=",sep="")\r\n+ as.numeric(gsub("^[^=]+= ","" ,ACQ[which(simplify2array(regexpr(regexpStr,ACQ))>0)]))\r\n+ }\r\n+ \r\n+ ACQFILE <- "acqus"\r\n+ SPECFILE <- paste(DataDir,"/1r",sep="")\r\n+ PROCFILE <- paste(DataDir,"/procs",sep="")\r\n+ \r\n+ ACQ <- readLines(ACQFILE)\r\n+ TD <- bruker.get_param(ACQ,"TD")\r\n+ SW <- bruker.get_param(ACQ,"SW")\r\n+ SWH <- bruker.get_param(ACQ,"SW_h")\r\n+ DTYPA <- bruker.get_param(ACQ,"DTYPA")\r\n+ BYTORDA <- bruker.get_param(ACQ,"BYTORDA")\r\n+ #ENDIAN = ifelse( BYTORDA==0, "little", "big")\r\n+ ENDIAN <- "little"\r\n+ SIZE = ifelse( DTYPA==0, 4, 8)\r\n+ \r\n+ PROC <- readLines(PROCFILE)\r\n+ OFFSET <- bruker.get_param(PROC,"OFFSET")\r\n+ SI <- bruker.get_param(PROC,"SI")\r\n+ \r\n+ to.read = file(SPECFILE,"rb")\r\n+ maxTDSI = max(TD,SI)\r\n+ # signal<-rev(readBin(to.read, what="int",size=SIZE, n=TD, signed = TRUE, endian = ENDIAN))\r\n+ signal<-rev(readBin(to.read, what="int",size=SIZE, n=maxTDSI, signed = TRUE, endian = ENDIAN))\r\n+ close(to.read)\r\n+ \r\n+ td <- length(signal)\r\n+ \r\n+ # dppm <- SW/(TD-1)\r\n+ dppm <- SW/(td-1)\r\n+ pmax <- OFFSET\r\n+ pmin <- OFFSET - SW\r\n+ ppmseq <- seq(from=pmin, to=pmax, by=dppm)\r\n+ signal <- 100*signal/max(signal)\r\n+ \r\n+ SampleSpectrum <- cbind(ppmseq,signal)\r\n+ return(SampleSpectrum)\r\n+ }\r\n+ \r\n+ ## SPECTRUM BUCKETING\r\n+ NmrBrucker_bucket <- function(spectrum)\r\n+ {\r\n+ # Initialisations\r\n+ b <- 1\r\n+ j <- 1\r\n+ # Variable number\r\n+ J <- round((spectrum[1,1]-spectrum[dim(spectrum)[1],1])/bucketSize)\r\n+ f.bucket <- matrix(rep(0,J*2),ncol=2)\r\n+ colnames(f.bucket) <- c("Bucket",FileNames[i])\r\n+ \r\n+ \r\n+ # Data bucketing\r\n+ while (j < dim(spectrum)[1])\r\n+ {\r\n+ # chemical shift\r\n+ BUB <- spectrum[j,1]\r\n+ \r\n+ # In zone exclusion?\r\n+ exclusion.in <- FALSE\r\n+ if (!is.null(exclusionZonesBorders))\r\n+ {\r\n+ for (k in 1:nrow(exclusion.zone.m))\r\n+ if (BUB <= exclusion.zone.m[k,1] && exclusion.zone.m['..b'if (exclusionZones == "yes")\r\n+ if (!is.null(exclusionZonesBorders))\r\n+ {\r\n+ exclusion.zone.m <- matrix(exclusionZonesBorders[[1]],nrow=1)\r\n+ if (length(exclusionZonesBorders) > 1)\r\n+ for (k in 2:length(exclusionZonesBorders))\r\n+ exclusion.zone.m <- rbind(exclusion.zone.m,exclusionZonesBorders[[k]])\r\n+ }\r\n+\r\n+ # Reading and Bucketing\r\n+ directory <- paste(directory,"/",sep="")\r\n+\r\n+ i <- 1\r\n+ while (i <= n)\r\n+ {\r\n+ # File reading\r\n+ SampleDir <- paste(directory,FileNames[i],"/1/",sep="")\r\n+ setwd(SampleDir)\r\n+ DataDir <- "pdata/1"\r\n+\r\n+ rawSpectrum <- NmRBrucker_read(DataDir,rawSpectrum)\r\n+\r\n+ orderedSpectrum <- rawSpectrum[order(rawSpectrum[,1],decreasing=T), ]\r\n+ \r\n+ # Removal of chemical shifts > leftBorder or < rightBorder boundaries\r\n+ truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]\r\n+ truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)\r\n+ \r\n+ # Bucketing\r\n+ spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)\r\n+ \r\n+ # spectrum Concatenation\r\n+ if (i == 1)\r\n+ bucketedSpectra <- spectrum.bucket\r\n+ if (i > 1)\r\n+ bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])\r\n+ colnames(bucketedSpectra)[i+1] <- FileNames[i]\r\n+ \r\n+ # Next sample\r\n+ rm(spectrum.bucket)\r\n+ i <- i +1\r\n+ }\r\n+ identifiants <- gsub("([- , * { } | \\\\[ ])","_",colnames(bucketedSpectra)[-1])\r\n+ colnames(bucketedSpectra) <- c(colnames(bucketedSpectra)[1],identifiants)\r\n+\r\n+ bucketedSpectra <- bucketedSpectra[bucketedSpectra[,1]!=0,]\r\n+ rownames(bucketedSpectra) <- paste("B",bucketedSpectra[,1],sep="")\r\n+ bucketedSpectra <- bucketedSpectra[,-1]\r\n+ \r\n+ # Metadata matrice outputs\r\n+ sampleMetadata <- data.frame(1:n)\r\n+ rownames(sampleMetadata) <- colnames(bucketedSpectra)\r\n+ colnames(sampleMetadata) <- "SampleOrder"\r\n+ \r\n+ variableMetadata <- data.frame(1:nrow(bucketedSpectra))\r\n+ rownames(variableMetadata) <- rownames(bucketedSpectra)\r\n+ colnames(variableMetadata) <- "VariableOrder"\r\n+\r\n+ # Directory\r\n+ cd(directory) \r\n+ \r\n+ # Bucketed spectra graph\r\n+ if (graph != "None")\r\n+ {\r\n+ # Graphic Device opening\r\n+ pdf(nomFichier,onefile=TRUE)\r\n+\r\n+ if (graph == "Overlay")\r\n+ {\r\n+ ymax <- max(bucketedSpectra)\r\n+ plot(1:length(bucketedSpectra[,1]),bucketedSpectra[,1],ylim=c(0,ymax),type=\'l\',col=1,xlab="Chemical shift",ylab="Intensity")\r\n+ for (i in 2:ncol(bucketedSpectra))\r\n+ {\r\n+ spectre <- bucketedSpectra[,i]\r\n+ lines(spectre,col=i)\r\n+ }\r\n+# legend(0,ymax,lty=c(1,1),legend=colnames(bucketedSpectra),col=1:ncol(bucketedSpectra))\r\n+ }\r\n+ else\r\n+ {\r\n+ for (i in 1:ncol(bucketedSpectra))\r\n+ {\r\n+ plot(1:length(bucketedSpectra[,i]),bucketedSpectra[,i],type=\'l\',col=1,xlab="Chemical shift",ylab="Intensity")\r\n+ }\r\n+ }\r\n+ dev.off()\r\n+ }\r\n+ return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,truncatedSpectrum_matrice\r\n+}\r\n+\r\n+\r\n+#################################################################################################################\r\n+## Typical function call\r\n+#################################################################################################################\r\n+## StudyDir <- "K:/PROJETS/Metabohub/Bruker/Tlse_BPASourisCerveau/"\r\n+## upper <- 9.5\r\n+## lower <- 0.8\r\n+## bucket.width <- 0.01\r\n+## exclusion <- TRUE\r\n+## exclusion.zone <- list(c(5.1,4.5))\r\n+## graphique <- "Overlay"\r\n+## nomFichier <- "Tlse_BPASourisCerveau_NmrBucketing_graph.pdf"\r\n+## tlse_cerveaupnd21.bucket <- NmrBucketing(StudyDir,upper,lower,bucket.width,exclusion,exclusion.zone,graphique,nomFichier)\r\n+## write.table(tlse_cerveaupnd21.bucket,file=paste(StudyDir,"Tlse_BPASourisCerveau_NmrBucketing_dataMatrix.tsv",sep=""),\r\n+## quote=FALSE,row.nmaes=FALSE,sep="\\t")\r\n+#################################################################################################################\r\n' |
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| diff -r 000000000000 -r a99a6026c972 NmrBucketing_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrBucketing_wrapper.R Fri Apr 08 10:56:14 2016 -0400 |
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| @@ -0,0 +1,156 @@ +#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file + +## 070115_NmrBucketing2galaxy_v1.R +## Marie Tremblay-Franco +## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics +## www.metabohub.fr/en +## marie.tremblay-franco@toulouse.inra.fr + +runExampleL <- FALSE + +if(runExampleL) { +##------------------------------ +## Example of arguments +##------------------------------ +argLs <- list(StudyDir = "Tlse_BPASourisCerveau", + upper = "10.0", + lower = "0.50", + bucket.width = "0.01", + exclusion = "TRUE", + exclusion.zone = list(c(6.5,4.5)), + graph="Overlay") + +argLs <- c(argLs, + list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""), + sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""), + variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""), + graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""), + logOut = paste(directory,"_NmrBucketing_log.txt",sep=""))) +} + +##------------------------------ +## Options +##------------------------------ +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + + +##------------------------------ +## Libraries laoding +##------------------------------ +# For parseCommandArgs function +library(batch) +# For cumtrapz function +library(pracma) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} +#Import the different functions +source_local("NmrBucketing_script.R") + +##------------------------------ +## Errors ????????????????????? +##------------------------------ + + +##------------------------------ +## Constants +##------------------------------ +topEnvC <- environment() +flagC <- "\n" + + +##------------------------------ +## Script +##------------------------------ +if(!runExampleL) + argLs <- parseCommandArgs(evaluate=FALSE) + +## sink(argLs[["logOut"]]) + + +## Parameters Loading +##------------------- + # Inputs +if (!is.null(argLs[["zipfile"]])){ + zipfile= argLs[["zipfile"]] + directory=unzip(zipfile, list=F) + directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") +} else if (!is.null(argLs[["library"]])){ + directory=argLs[["library"]] + if(!file.exists(directory)){ + error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.") + print(error_message) + stop(error_message) + } +} + +leftBorder <- argLs[["left_border"]] +rightBorder <- argLs[["right_border"]] +bucketSize <- argLs[["bucket_width"]] +exclusionZones <- argLs[["zone_exclusion_choices.choice"]] + +exclusionZonesBorders <- NULL +if (!is.null(argLs$zone_exclusion_left)) +{ + for(i in which(names(argLs)=="zone_exclusion_left")) + { + exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) + } +} + +graphique <- argLs[["graphType"]] + + # Outputs +nomGraphe <- argLs[["graphOut"]] +dataMatrixOut <- argLs[["dataMatrixOut"]] +sampleMetadataOut <- argLs[["sampleOut"]] +variableMetadataOut <- argLs[["variableOut"]] +log <- argLs[["logOut"]] + +## Checking arguments +##------------------- +error.stock <- "\n" + +if(length(error.stock) > 1) + stop(error.stock) + + +## Computation +##------------ +outputs <- NmrBucketing(directory,leftBorder,rightBorder,bucketSize,exclusionZones,exclusionZonesBorders,graphique,nomGraphe,log) +data_bucket <- outputs[[1]] +data_sample <- outputs[[2]] +data_variable <- outputs[[3]] + +## Saving +##------- + # Data +data_bucket <- cbind(rownames(data_bucket),data_bucket) +colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1]) +write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t") + # Sample +data_sample <- cbind(rownames(data_sample),data_sample) +colnames(data_sample) <- c("Sample",colnames(data_sample)[-1]) +write.table(data_sample,file=argLs$sampleOut,quote=FALSE,row.names=FALSE,sep="\t") + # Variable +data_variable <- cbind(rownames(data_variable),data_variable) +colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1]) +write.table(data_variable,file=argLs$variableOut,quote=FALSE,row.names=FALSE,sep="\t") + + +## Ending +##--------------------- + +cat("\nEnd of 'NMR bucketing' Galaxy module call: ", as.character(Sys.time()), sep = "") + +## sink(NULL) + +options(stringsAsFactors = strAsFacL) + +rm(list = ls()) |
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| diff -r 000000000000 -r a99a6026c972 NmrBucketing_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrBucketing_xml.xml Fri Apr 08 10:56:14 2016 -0400 |
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| b'@@ -0,0 +1,279 @@\n+<tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.1">\r\n+\r\n+ <description> Bucketing and integration of NMR Bruker raw data</description>\r\n+\r\n+ <requirements>\r\n+ <requirement type="package" version="3.1.2">R</requirement>\r\n+\t <requirement type="package" version="1.1_4">r-batch</requirement>\r\n+\t <requirement type="package" version="1.8.8">r-pracma</requirement>\r\n+ </requirements>\r\n+\r\n+ <stdio>\r\n+ <exit_code range="1:" level="fatal" />\r\n+ </stdio>\r\n+\r\n+ <command>\r\n+ Rscript $__tool_directory__/NmrBucketing_wrapper.R\r\n+\r\n+ #if $inputs.input == "lib":\r\n+ library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library\r\n+ #elif $inputs.input == "zip_file":\r\n+ zipfile $inputs.zip_file\r\n+ #end if\r\n+\r\n+\r\n+ ## Bucket width\r\n+ bucket_width $bucket_width\r\n+\r\n+ ## Spectra borders\r\n+ left_border $left_border\r\n+ right_border $right_border\r\n+\r\n+\r\n+ ## Spectra representation\r\n+ graphType $graphType\r\n+\r\n+ ## Exclusion zone\r\n+ zone_exclusion_choices.choice ${zone_exclusion_choices.choice}\r\n+ #if str($zone_exclusion_choices.choice) == \'yes\':\r\n+ #for $i in $zone_exclusion_choices.conditions:\r\n+ zone_exclusion_left ${i.zone_exclusion_left}\r\n+ zone_exclusion_right ${i.zone_exclusion_right}\r\n+ #end for\r\n+ #end if\r\n+\r\n+ ## Outputs\r\n+ logOut log.log\r\n+ dataMatrixOut $dataMatrixOut\r\n+ sampleOut $sampleOut\r\n+ variableOut $variableOut\r\n+ graphOut $graphOut; cat log.log\r\n+ </command>\r\n+\r\n+ <inputs>\r\n+ <conditional name="inputs">\r\n+ <param name="input" type="select" label="Choose your inputs method" >\r\n+ <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>\r\n+ <option value="lib" >Library directory name</option>\r\n+ </param>\r\n+ <when value="zip_file">\r\n+ <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />\r\n+ </when>\r\n+ <when value="lib">\r\n+ <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >\r\n+ <validator type="empty_field"/> \r\n+ </param>\r\n+ </when>\r\n+\r\n+ </conditional>\r\n+\r\n+ <param name="bucket_width" label="Bucket width" type="float" value="0.04" help="Default value is 0.04 ppm"/>\r\n+\r\n+ <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>\r\n+ <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>\r\n+\r\n+ <conditional name="zone_exclusion_choices">\r\n+ <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >\r\n+ <option value="yes" > yes </option>\r\n+ <option value="no" selected="true"> no </option>\r\n+ </param>\r\n+ <when value="yes">\r\n+ <repeat name="conditions" title="exclusion zones">\r\n+ <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />\r\n+ <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />\r\n+ </repeat>\r\n+ </when>\r\n+ <when value="no">\r\n+ </when>\r\n+ </conditional>\r\n+\r\n+ <param name="graphType" label="Spectra representation" type="select" help="Select \'None\' for no representation,\'Overlay\' to overlay all spectra on a unique chart and \'One per individual\' to generate an individual chart for each observation">\r\n+ <option value="None"> none '..b'---+----------------------+--------+\r\n+| Name | Output file | Format |\r\n++===========================+======================+========+\r\n+|NmrNormalization | dataMatrix.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+|Univariate | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+|Multivariate | sampleMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+| | variableMetadata.tsv | Tabular|\r\n++---------------------------+----------------------+--------+\r\n+\r\n+\r\n+-----------\r\n+Input files\r\n+-----------\r\n+\r\n++---------------------------+------------+\r\n+| Parameter : num + label | Format |\r\n++===========================+============+\r\n+| 1 : Choose your inputs | zip |\r\n++---------------------------+------------+\r\n+\r\n+**Choose your inputs**\r\n+\r\n+You have two methods for your inputs:\r\n+\r\n+| Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).\r\n+| library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.\r\n+\r\n+.. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png\r\n+:width: 800\r\n+\r\n+----------\r\n+Parameters\r\n+----------\r\n+\r\n+Bucket width\r\n+| size of windows\r\n+|\r\n+\r\n+Left limit\r\n+| Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm\r\n+|\r\n+\r\n+Right limit\r\n+| Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm\r\n+|\r\n+\r\n+Exclusion zone(s)\r\n+| Spectral regions to exclude, water, solvents, ... resonance\r\n+| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,\r\n+| If NO: no zone to exclude\r\n+| Default value is NO\r\n+|\r\n+\r\n+Left exclusion zone\r\n+| Upper boundary of exclusion zone\r\n+|\r\n+\r\n+Right exclusion zone\r\n+| Lower boundary of exclusion zone\r\n+\r\n+| *Notes:* \r\n+| - these parameters can be used several times using the "Add new exclusion zones" button\r\n+|\r\n+\r\n+Spectra representation:\r\n+| Graphical chart of bucketed and integrated raw files\r\n+| If "Overlay": the n (sample number) spectra are overlaid on the same figure\r\n+| If "One_per_individual": pdf file includes n pages (1 per sample)\r\n+|\r\n+\r\n+\r\n+------------\r\n+Output files\r\n+------------\r\n+\r\n+\r\n+bucketedData.tsv\r\n+| tabular output\r\n+| Data matrix with p rows (buckets) and n columns (samples) containing the intensities\r\n+|\r\n+\r\n+sampleMetadata.tsv\r\n+| tabular output\r\n+| file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order: the rownames of sampleMetadata must be identical to the colnames of the bucketedData. Can add columns with numeric and/or character sample metadata. This file is optional in the normalization step and mandatory in the statistical analysis step of the workflow.\r\n+|\r\n+\r\n+variableMetadata.tsv\r\n+| tabular output\r\n+| file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order: the rownames of variableMetadata must be identical to the rownames of the bucketedData. Can add columns with numeric and/or character variable metadata. This file is mandatory in the statistical analysis step of the workflow.\r\n+|\r\n+\r\n+spectra.pdf\r\n+| pdf output\r\n+| Graphical chart of bucketed and integrated data\r\n+| \r\n+\r\n+\r\n+---------------------------------------------------\r\n+\r\n+---------------\r\n+Working example\r\n+---------------\r\n+\r\n+\r\n+.. class:: warningmark\r\n+\r\n+Under construction\r\n+\r\n+.. image:: ./static/images/Mth_Travaux.png\r\n+:width: 100\r\n+\r\n+\r\n+ </help>\r\n+ <citations>\r\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\r\n+ </citations>\r\n+</tool>\r\n+\r\n' |
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| diff -r 000000000000 -r a99a6026c972 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Apr 08 10:56:14 2016 -0400 |
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| @@ -0,0 +1,20 @@ + +Changelog/News +-------------- + +**Version 1.0.1 - 04/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + +**Version 2015-01-08 - 08/01/2015** + + + +Test Status +----------- + +Planemo test using conda: passed + +Planemo shed_test: passed + |
| b |
| diff -r 000000000000 -r a99a6026c972 planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Fri Apr 08 10:56:14 2016 -0400 |
| [ |
| @@ -0,0 +1,12 @@ +planemo conda_init +planemo conda_install . +planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev" + +#All 1 test(s) executed passed. +#nmr_bucketing[0]: passed + + +planemo shed_test -t testtoolshed --install_galaxy --galaxy_branch "dev" + +#All 1 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/nmr_bucketing/NmrBucketing/1.0.1[0]: passed |
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| diff -r 000000000000 -r a99a6026c972 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Apr 08 10:56:14 2016 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r a99a6026c972 static/images/MTH - Architecture repertoire Bruker.png |
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| Binary file static/images/MTH - Architecture repertoire Bruker.png has changed |
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| diff -r 000000000000 -r a99a6026c972 static/images/Mth_Travaux.png |
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| Binary file static/images/Mth_Travaux.png has changed |
| b |
| diff -r 000000000000 -r a99a6026c972 test-data/MTBLS1.zip |
| b |
| Binary file test-data/MTBLS1.zip has changed |
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| diff -r 000000000000 -r a99a6026c972 test-data/MTBLS1_bucketedData.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_bucketedData.tabular Fri Apr 08 10:56:14 2016 -0400 |
| b |
| b'@@ -0,0 +1,595 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| diff -r 000000000000 -r a99a6026c972 test-data/MTBLS1_sampleMetadata.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_sampleMetadata.tabular Fri Apr 08 10:56:14 2016 -0400 |
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| @@ -0,0 +1,24 @@ +Sample SampleOrder +ADG10003u_007 1 +ADG10003u_008 2 +ADG10003u_009 3 +ADG10003u_010 4 +ADG10003u_015 5 +ADG10003u_016 6 +ADG10003u_017 7 +ADG10003u_021 8 +ADG10003u_022 9 +ADG10003u_023 10 +ADG10003u_051 11 +ADG10003u_052 12 +ADG10003u_053 13 +ADG10003u_066 14 +ADG10003u_067 15 +ADG10003u_071 16 +ADG10003u_072 17 +ADG10003u_073 18 +ADG10003u_087 19 +ADG10003u_088 20 +ADG10003u_089 21 +ADG10003u_097 22 +ADG10003u_098 23 |
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| diff -r 000000000000 -r a99a6026c972 test-data/MTBLS1_variableMetadata.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_variableMetadata.tabular Fri Apr 08 10:56:14 2016 -0400 |
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| b |
| diff -r 000000000000 -r a99a6026c972 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Apr 08 10:56:14 2016 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?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="r-pracma" version="1.8.8"> + <repository changeset_revision="48eb1ff95b33" name="package_r_pracma_1_8_8" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
