Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing
changeset 12:4d5c06b46c2f draft default tip
Uploaded
| author | marie-tremblay-metatoul |
|---|---|
| date | Thu, 10 Aug 2017 05:21:09 -0400 |
| parents | ed40bbda7959 |
| children | |
| files | nmr_bucketing/.Rhistory nmr_bucketing/NmrBucketing_script.R nmr_bucketing/NmrBucketing_wrapper.R nmr_bucketing/NmrBucketing_xml.xml nmr_bucketing/README.rst nmr_bucketing/planemo_test.sh nmr_bucketing/test-data/MTBLS1_bucketedData.tabular nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular |
| diffstat | 7 files changed, 902 insertions(+), 325 deletions(-) [+] |
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--- a/nmr_bucketing/NmrBucketing_script.R Fri May 05 07:08:14 2017 -0400 +++ b/nmr_bucketing/NmrBucketing_script.R Thu Aug 10 05:21:09 2017 -0400 @@ -251,8 +251,13 @@ rownames(variableMetadata) <- rownames(bucketedSpectra) colnames(variableMetadata) <- "VariableOrder" - - return(list(bucketedSpectra,sampleMetadata,variableMetadata,ppm)) # ,truncatedSpectrum_matrice + if (fileType=="zip") + { + return(list(bucketedSpectra,sampleMetadata,variableMetadata,ppm)) + } else + { + return(list(bucketedSpectra,variableMetadata,ppm)) + } }
--- a/nmr_bucketing/NmrBucketing_wrapper.R Fri May 05 07:08:14 2017 -0400 +++ b/nmr_bucketing/NmrBucketing_wrapper.R Thu Aug 10 05:21:09 2017 -0400 @@ -39,7 +39,7 @@ ## Libraries laoding ##------------------------------ # For parseCommandArgs function -library(batch) +library(batch) # For cumtrapz function library(pracma) @@ -81,14 +81,7 @@ zipfile= argLs[["zipfile"]] directory=unzip(zipfile, list=F) directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") -} else if (!is.null(argLs[["library"]])){ - fileType="zip" - 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) - } + sampleMetadataOut <- argLs[["sampleOut"]] } else if (!is.null(argLs[["tsvfile"]])){ fileType="tsv" directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t") @@ -114,11 +107,19 @@ nomGraphe <- argLs[["graphOut"]] dataMatrixOut <- argLs[["dataMatrixOut"]] logFile <- argLs[["logOut"]] -if (fileType=="zip") -{ - sampleMetadataOut <- argLs[["sampleOut"]] - variableMetadataOut <- argLs[["variableOut"]] +variableMetadataOut <- argLs[["variableOut"]] + +## Checking R packages +##-------------------- +sink(logFile) +cat("\t PACKAGE INFO \n") +pkgs=c("batch","pracma") +for(pkg in pkgs) { + suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") } +cat("\n") + ## Checking arguments ##------------------- @@ -126,18 +127,25 @@ if(length(error.stock) > 1) stop(error.stock) - - + + ## Computation ##------------ -outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize, - exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe, +outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize, + exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe, savLog.txtC=logFile) data_bucket <- outputs[[1]] -data_sample <- outputs[[2]] -data_variable <- outputs[[3]] -ppm <- outputs[[4]] -ppm <- round(ppm,2) +if (fileType=="zip") +{ + data_sample <- outputs[[2]] + data_variable <- outputs[[3]] + ppm <- outputs[[4]] +} else +{ + data_variable <- outputs[[2]] + ppm <- outputs[[3]] +} +ppm <- round(ppm,1) ## Graphical outputs ##------------------ @@ -154,20 +162,33 @@ # Graphic Device opening pdf(nomGraphe,onefile=TRUE) - + graphical.zone.length <- length(exclusionZonesBorders) if (graphique == "Overlay") { # Global spectral window spectra <- data.frame(t(data_bucket)) drawSpec(spectra,xlab="", ylab="Intensity", main="") + ## Zoomed spectral window depending on exclusion zone(s) + if (nbZones != 0) + { + n <- length(excludedZone) + drawSpec(spectra[,1:which(ppm == round(excludedZone[n],1))[1]],xlab="", ylab="spectra", main="") + n <- n - 1 + while (n >= nbZones & nbZones > 1) + { + drawSpec(spectra[,(which(ppm == round(excludedZone[n],1)[1])):(which(ppm == round(excludedZone[n-1],1)[1]))],xlab="", ylab="spectra", main="") + n <- n - 2 + } + drawSpec(spectra[,(which(ppm == round(excludedZone[1])[1],1)):ncol(spectra)],xlab="", ylab="spectra", main="") + } } else { for (i in 1:ncol(data_bucket)) { -## par(mfrow=c((nbZones+2),1)) + par(mfrow=c((graphical.zone.length+2),1)) n <- length(excludedZone) spectra <- t(data_bucket[,i]) names(spectra) <- rownames(data_bucket) @@ -181,10 +202,54 @@ xPos = c(0:nAxisPos) * tempVal axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP]) - - } + ## Zoomed spectral window depending on exclusion zone(s) + for (g in 1:graphical.zone.length) + { + spectra <- t(data_bucket[,i]) + names(spectra) <- rownames(data_bucket) + if (g==1) + { + plot(1:length(spectra[1:(which(ppm == round(exclusionZonesBorders[[g]][1],1))[1])]), + spectra[1:(which(ppm == round(exclusionZonesBorders[[g]][1],1))[1])], type='l', xlab="", ylab="Intensity", main="", xaxt = "n") + xPos <- 1 + nAxisPos <- 4 + startP <- length(nAxisPos) + endP <- length(1:(which(ppm == round(exclusionZonesBorders[[g]][1],1))[1])) + GraphRange <- c(startP:endP) + tempVal = trunc(length(GraphRange)/nAxisPos) + xPos = c(0:nAxisPos) * tempVal + axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP]) + } else + { + plot(1:length(spectra[(which(ppm == round(exclusionZonesBorders[[g-1]][2],1))[1]):(which(ppm == round(exclusionZonesBorders[[g]][1],1))[1])]), + spectra[(which(ppm == round(exclusionZonesBorders[[g-1]][2],1))[1]):(which(ppm == round(exclusionZonesBorders[[g]][1],1))[1])], + type='l', xlab="", ylab="Intensity", main="", xaxt = "n") + xPos <- 1 + nAxisPos <- 4 + startP <- length(nAxisPos) + endP <- length(spectra[(which(ppm == round(exclusionZonesBorders[[g-1]][2],1))[1]):(which(ppm == round(exclusionZonesBorders[[g]][1],1))[1])]) + GraphRange <- c(startP:endP) + tempVal = trunc(length(GraphRange)/nAxisPos) + xPos = c(0:nAxisPos) * tempVal + noms <- rownames(data_bucket)[xPos + which(ppm == round(exclusionZonesBorders[[g-1]][2],1))[1]] + axis(1, at = xPos, labels = noms) + } + } + plot(1:length(spectra[(which(ppm == round(exclusionZonesBorders[[g]][2],1))[1]):nrow(data_bucket)]), + spectra[(which(ppm == round(exclusionZonesBorders[[g]][2],1))[1]):nrow(data_bucket)], type='l', xlab="", ylab="Intensity", main="", xaxt = "n") + xPos <- 1 + nAxisPos <- 4 + startP <- length(nAxisPos) + endP <- length((which(ppm == round(exclusionZonesBorders[[g]][2],1))[1]):nrow(data_bucket)) + GraphRange <- c(startP:endP) + tempVal = trunc(length(GraphRange)/nAxisPos) + xPos = c(0:nAxisPos) * tempVal + noms <- c(rownames(data_bucket)[xPos[-5] + which(ppm == round(exclusionZonesBorders[[g]][2],1))[1]], rownames(data_bucket)[which(ppm == rightBorder)[1]]) + print(noms) + axis(1, at = xPos, labels = noms) + } } - dev.off() + invisible(dev.off()) } ## Saving @@ -193,25 +258,22 @@ data_bucket <- cbind(rownames(data_bucket),data_bucket) colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1]) write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t") + # Sample if (fileType=="zip") { - # Sample - data_sample <- cbind(rownames(data_sample),data_sample) - colnames(data_sample) <- c("Sample",colnames(data_sample)[-1]) - write.table(data_sample,file=argLs$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$variableOut,quote=FALSE,row.names=FALSE,sep="\t") + data_sample <- cbind(rownames(data_sample),data_sample) + colnames(data_sample) <- c("Sample",colnames(data_sample)[-1]) + write.table(data_sample,file=argLs$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$variableOut,quote=FALSE,row.names=FALSE,sep="\t") + ## Ending ##--------------------- - cat("\nEnd of 'NMR bucketing' Galaxy module call: ", as.character(Sys.time()), sep = "") - -## sink(NULL) - +sink() options(stringsAsFactors = strAsFacL) - rm(list = ls())
--- a/nmr_bucketing/NmrBucketing_xml.xml Fri May 05 07:08:14 2017 -0400 +++ b/nmr_bucketing/NmrBucketing_xml.xml Thu Aug 10 05:21:09 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.3"> +<tool id="NmrBucketing" name="NMR_Bucketing" version="2.0.3"> <description> Bucketing and integration of NMR Bruker raw data</description> @@ -20,7 +20,6 @@ zipfile '$inputs.zip_file' #end if - ## Bucket width bucket_width $bucket_width @@ -28,10 +27,6 @@ left_border $left_border right_border $right_border - - ## Spectra representation - graphType $graphType - ## Exclusion zone zone_exclusion_choices.choice ${zone_exclusion_choices.choice} #if str($zone_exclusion_choices.choice) == 'yes': @@ -41,12 +36,15 @@ #end for #end if + ## Spectra representation + graphType $graphType + ## Outputs - logOut log.log + logOut $logOut dataMatrixOut '$dataMatrixOut' sampleOut '$sampleOut' variableOut '$variableOut' - graphOut '$graphOut'; cat log.log + graphOut '$graphOut' </command> <inputs> @@ -92,6 +90,7 @@ </inputs> <outputs> + <data format="txt" name="logOut" label="${tool.name}_log" /> <data format="tabular" name="sampleOut" label="${tool.name}_sampleMetadata" /> <data format="tabular" name="variableOut" label="${tool.name}_variableMetadata" /> <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" /> @@ -270,6 +269,13 @@ Changelog/News -------------- +**Version 2.0.3 - 10/08/2017** + +- BUG CORRECTION: “zoomed” representations: x-axis labels + sampleMetadata output: empty + +**Version 2.0.2 - 21/04/2017** + +- IMPROVEMENT: Add “zoomed” representations of bucketed spectra, depending on exclusion zone borders **Version 1.0.3 - 24/10/2016**
--- a/nmr_bucketing/README.rst Fri May 05 07:08:14 2017 -0400 +++ b/nmr_bucketing/README.rst Thu Aug 10 05:21:09 2017 -0400 @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 2.0.2 - 21/04/2017** + +- IMPROVEMENT: Add “zoomed” representations of bucketed spectra, depending on exclusion zone borders + **Version 1.0.3 - 24/10/2016** - ENHANCEMENT: add possibility of bucketing processed files (upstream tools)
--- a/nmr_bucketing/planemo_test.sh Fri May 05 07:08:14 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -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
--- a/nmr_bucketing/test-data/MTBLS1_bucketedData.tabular Fri May 05 07:08:14 2017 -0400 +++ b/nmr_bucketing/test-data/MTBLS1_bucketedData.tabular Thu Aug 10 05:21:09 2017 -0400 @@ -329,6 +329,182 @@ B6.026 0.000159319062283075 0.000446721409572097 0.000382633919227815 0.000126942645667836 0.000166313059734916 8.94758281061922e-05 0.000385838304457983 2.87763377558405e-05 0.000360994039934173 0.000144325493649279 0.000361987046197092 0.000483733340109536 0.000297916109701254 0.00053237165368555 0.000472963510270079 0.000780680118728634 0.00048247577268934 0.000479026836151301 0.000622055982981826 0.000302910238854912 0.000343759407196818 0.000314304432305254 0.000481969249797228 B6.016 0.000205982599932515 0.00039803027868312 0.000331140965056563 0.000138075073133353 0.000217185180911849 0.000104037016792196 0.000398311763845808 1.16037245322327e-05 0.000447143055443722 0.000159497854969022 0.000371762570375265 0.000465691083996931 0.000299910086232853 0.00061280087605037 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