# HG changeset patch
# User marie-tremblay-metatoul
# Date 1502356869 14400
# Node ID 4d5c06b46c2fca04844b0f4f828b14e8ede995b2
# Parent  ed40bbda7959e296b411469cf60e798ee80df73c
Uploaded

diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/.Rhistory
diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/NmrBucketing_script.R
--- 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))
+  }
 }
 
 
diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/NmrBucketing_wrapper.R
--- 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())
diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/NmrBucketing_xml.xml
--- 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**
 
diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/README.rst
--- 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)
diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/planemo_test.sh
--- 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
diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/test-data/MTBLS1_bucketedData.tabular
--- 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
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diff -r ed40bbda7959 -r 4d5c06b46c2f nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular
--- a/nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular	Fri May 05 07:08:14 2017 -0400
+++ b/nmr_bucketing/test-data/MTBLS1_variableMetadata.tabular	Thu Aug 10 05:21:09 2017 -0400
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