changeset 1:d9e05021553c draft

planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
author ethevenot
date Sat, 06 Aug 2016 12:02:52 -0400
parents eacea1349a7c
children 0ccfc3e15710
files README.md runit/input/dataMatrix.tsv runit/output/dataMatrix.tsv runit/output/information.txt runit/transformation_runtests.R runit/transformation_tests.R tests/input/dataMatrix.tsv tests/transformation_tests.R transformation_config.xml transformation_script.R transformation_wrapper.R
diffstat 11 files changed, 340 insertions(+), 359 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Fri Jul 29 12:11:01 2016 -0400
+++ b/README.md	Sat Aug 06 12:02:52 2016 -0400
@@ -1,12 +1,14 @@
-## Transformation of the data matrix  
-#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project
+Transformation of the data matrix  
+=================================
+
+A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure  
 
 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/transformation.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/transformation).
 
 ### Description
 
-**Version:** 2.0.2  
-**Date:** 2016-07-27  
+**Version:** 2.2.0  
+**Date:** 2016-08-04  
 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)   
 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)  
 **Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354)  
@@ -16,23 +18,39 @@
 
 ### Installation
 
-* Configuration file: **transformation_config.xml**
-* Image files: **static/images/transformation_workflowPositionImage.png**   
-* Wrapper file: **transformation_wrapper.R**  
+* Configuration file: `transformation_config.xml`  
+* Image files: `static/images/transformation_workflowPositionImage.png`   
+* Wrapper file: `transformation_wrapper.R`  
 * R packages  
     + **batch** from CRAN  
-> install.packages("batch", dep=TRUE)   
-
+ 
+    ```r
+    install.packages("batch", dep=TRUE)  
+    ```
+    
 ### Tests
 
-The code in the wrapper can be tested by running the **tests/transformation_tests.R** in R  
+The code in the wrapper can be tested by running the `runit/transformation_runtests.R` R file
+
+You will need to install **RUnit** package in order to make it run:
+```r
+install.packages('RUnit', dependencies = TRUE)
+```
+
+### Working example
+
+See the **W4M00001b_sacurine-complete** or **W4M00002_mtbls2** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)  
 
 ### News
 
+##### CHANGES IN VERSION 2.2.0  
+
+NEW FEATURE  
+
+ * Square root transformation now available  
+
 ##### CHANGES IN VERSION 2.0.2  
 
 INTERNAL MODIFICATION  
 
-    o Creating tests for R code  
-    
-***
\ No newline at end of file
+ * Creating tests for R code  
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/dataMatrix.tsv	Sat Aug 06 12:02:52 2016 -0400
@@ -0,0 +1,4 @@
+dataMatrix	HU_017	HU_021	HU_027	HU_032	HU_041	HU_048	HU_049	HU_050	HU_052	HU_059	HU_060	HU_066	HU_072	HU_077	HU_090	HU_109	HU_110	HU_125	HU_126	HU_131	HU_134	HU_149	HU_150	HU_173	HU_179	HU_180	HU_182	HU_202	HU_204	HU_209
+HMDB01032	2569204.92420381	0	NA	1258838.24348419	13039543.0754619	1909391.77026598	3495.09386434063	2293521.90928998	128503.275117713	81872.5276382213	8103557.56578035	149574887.036181	1544036.41049333	7103429.53933206	14138796.50382	NA	263054.73056162	1671332.30008058	88433.1944958815	23602331.2894815	18648126.5206986	1554657.98756878	34152.3646391152	209372.71275317	33187733.370626	202438.591636003	13581070.0886437	354170.810678102	9120781.48986975	43419175.4051586
+HMDB03072	3628416.30251025	65626.9834353751	112170.118946651	3261804.34422417	42228.2787747563	343254.201250707	1958217.69317664	11983270.0435677	5932111.41638028	5511385.83359531	9154521.47755199	2632133.21209418	9500411.14556502	6551644.51726592	7204319.80891836	1273412.04795188	0	8932005.5351622	8340827.52597275	NA	11217839.169041	5919262.81433556	11790077.0657915	9567977.80797097	73717.5811684739	9991787.29074293	4208098.14739633	623970.649925847	10904221.2642849	2171793.93621067
+HMDB00792	429568.609438384	3887629.50527037	1330692.11658995	1367446.73023821	844197.447472453	2948090.71886592	1614157.90566884	3740009.19379795	3292251.66531919	2310688.79492013	4404239.59008605	3043289.12780863	825736.467181043	2523241.91730649	NA	474901.604069803	0	2955990.64049134	1917716.3427982	1767962.67737699	5926203.40397675	1639065.69474684	346810.763557826	1054776.22313737	2390258.27543894	1831346.37315857	1026696.36904362	7079792.50047866	4368341.01359769	3495986.87280275
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/dataMatrix.tsv	Sat Aug 06 12:02:52 2016 -0400
@@ -0,0 +1,4 @@
+dataMatrix	HU_017	HU_021	HU_027	HU_032	HU_041	HU_048	HU_049	HU_050	HU_052	HU_059	HU_060	HU_066	HU_072	HU_077	HU_090	HU_109	HU_110	HU_125	HU_126	HU_131	HU_134	HU_149	HU_150	HU_173	HU_179	HU_180	HU_182	HU_202	HU_204	HU_209
+HMDB01032	1602.87395767846	0	NA	1121.97960921052	3611.03074972533	1381.80742879244	59.1193188758178	1514.43781955219	358.473534752167	286.133758298844	2846.6748261402	12230.0812358782	1242.592616465	2665.22598278871	3760.15910618421	NA	512.888614185985	1292.80017793957	297.377192292687	4858.22305884379	4318.34766093452	1246.85924930153	184.803583945537	457.572631123377	5760.87956571095	449.931763310841	3685.25034273707	595.122517367728	3020.063159914	6589.32283358151
+HMDB03072	1904.84023017949	256.177640389194	334.91807796333	1806.04660632669	205.495203775554	585.878998813498	1399.36331707553	3461.68601169541	2435.59262118694	2347.63409278263	3025.64397732978	1622.38503817503	3082.27369738072	2559.61804128388	2684.0864011649	1128.45560300434	0	2988.64610403477	2888.04908648949	NA	3349.30428134575	2432.95351668205	3433.66816477532	3093.21480145996	271.50981781231	3160.97885009421	2051.36494739389	789.918128622104	3302.1540340034	1473.70076209883
+HMDB00792	655.414837670299	1971.70725648367	1153.55629103653	1169.37877962541	918.802180816117	1717.00050054329	1270.49514193044	1933.91033757978	1814.45630019551	1520.09499536053	2098.62802566011	1744.50254451194	908.700427633355	1588.47156641423	NA	689.131049996881	0	1719.29946213315	1384.81635706624	1329.64757638142	2434.37947000396	1280.26001060208	588.906413242228	1027.0229905593	1546.04601336407	1353.27246818908	1013.26026717898	2660.78794729656	2090.05765796011	1869.75583240239
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/information.txt	Sat Aug 06 12:02:52 2016 -0400
@@ -0,0 +1,10 @@
+
+Start of the 'Transformation' module: Thu 04 Aug 2016 08:58:11 PM
+
+Missing values in the 'dataMatrix': 4 (4%)
+
+Zero values in the 'dataMatrix': 3 (3%)
+
+'Square root' transformation
+
+End of the 'Transformation' Galaxy module call: Thu 04 Aug 2016 08:58:11 PM
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/transformation_runtests.R	Sat Aug 06 12:02:52 2016 -0400
@@ -0,0 +1,102 @@
+#!/usr/bin/env Rscript
+
+## Package
+##--------
+
+library(RUnit)
+
+## Constants
+##----------
+
+testOutDirC <- "output"
+argVc <- commandArgs(trailingOnly = FALSE)
+scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
+
+
+## Functions
+##-----------
+
+## Reading tables (matrix or data frame)
+readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
+
+    	file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
+
+        switch(typeC,
+               matrix = return(t(as.matrix(read.table(file = fileC,
+                   header = TRUE,
+                   row.names = 1,
+                   sep = "\t",
+                   stringsAsFactors = FALSE)))),
+               dataframe = return(read.table(file = fileC,
+                   header = TRUE,
+                   row.names = 1,
+                   sep = "\t",
+                   stringsAsFactors = FALSE)))
+
+}
+
+## Call wrapper
+wrapperCallF <- function(paramLs) {
+
+	## Set program path
+    	wrapperPathC <- file.path(dirname(scriptPathC), "..", "transformation_wrapper.R")
+
+	## Set arguments
+	argLs <- NULL
+	for (parC in names(paramLs))
+		argLs <- c(argLs, parC, paramLs[[parC]])
+
+	## Call
+	wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
+
+        if(.Platform$OS.type == "windows")
+            wrapperCallC <- paste("Rscript", wrapperCallC)
+
+	wrapperCodeN <- system(wrapperCallC)
+
+	if (wrapperCodeN != 0)
+		stop("Error when running transformation_wrapper.R.")
+
+	## Get output
+	outLs <- list()
+	if ("dataMatrix_out" %in% names(paramLs))
+            outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
+	if ("sampleMetadata_out" %in% names(paramLs))
+            outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
+	if ("variableMetadata_out" %in% names(paramLs))
+            outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
+        if("information" %in% names(paramLs))
+            outLs[["infVc"]] <- readLines(paramLs[["information"]])
+
+	return(outLs)
+}
+
+## Setting default parameters
+defaultArgF <- function(testInDirC) {
+
+    defaultArgLs <- list()
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
+        defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
+        defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
+        defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
+
+    defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
+    defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
+
+    defaultArgLs
+
+}
+
+## Main
+##-----
+
+## Create output folder
+file.exists(testOutDirC) || dir.create(testOutDirC)
+
+## Run tests
+test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
+isValidTestSuite(test.suite)
+test.results <- runTestSuite(test.suite)
+print(test.results)
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/transformation_tests.R	Sat Aug 06 12:02:52 2016 -0400
@@ -0,0 +1,24 @@
+test_input_log10 <- function() {
+
+    testDirC <- "input"
+    argLs <- list(method = "log10")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+
+    checkEqualsNumeric(outLs[['datMN']]['HU_021', 'HMDB03072'], 4.817089, tolerance = 1e-6)
+ 
+}
+
+test_input_sqrt <- function() {
+
+    testDirC <- "input"
+    argLs <- list(method = "sqrt")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+
+    checkEqualsNumeric(outLs[['datMN']]['HU_021', 'HMDB03072'], 256.177640, tolerance = 1e-6)
+ 
+}
+
--- a/tests/input/dataMatrix.tsv	Fri Jul 29 12:11:01 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-dataMatrix	HU_017	HU_021	HU_027	HU_032	HU_041	HU_048	HU_049	HU_050	HU_052	HU_059	HU_060	HU_066	HU_072	HU_077	HU_090	HU_109	HU_110	HU_125	HU_126	HU_131	HU_134	HU_149	HU_150	HU_173	HU_179	HU_180	HU_182	HU_202	HU_204	HU_209
-HMDB01032	2569204.92420381	0	NA	1258838.24348419	13039543.0754619	1909391.77026598	3495.09386434063	2293521.90928998	128503.275117713	81872.5276382213	8103557.56578035	149574887.036181	1544036.41049333	7103429.53933206	14138796.50382	NA	263054.73056162	1671332.30008058	88433.1944958815	23602331.2894815	18648126.5206986	1554657.98756878	34152.3646391152	209372.71275317	33187733.370626	202438.591636003	13581070.0886437	354170.810678102	9120781.48986975	43419175.4051586
-HMDB03072	3628416.30251025	65626.9834353751	112170.118946651	3261804.34422417	42228.2787747563	343254.201250707	1958217.69317664	11983270.0435677	5932111.41638028	5511385.83359531	9154521.47755199	2632133.21209418	9500411.14556502	6551644.51726592	7204319.80891836	1273412.04795188	0	8932005.5351622	8340827.52597275	NA	11217839.169041	5919262.81433556	11790077.0657915	9567977.80797097	73717.5811684739	9991787.29074293	4208098.14739633	623970.649925847	10904221.2642849	2171793.93621067
-HMDB00792	429568.609438384	3887629.50527037	1330692.11658995	1367446.73023821	844197.447472453	2948090.71886592	1614157.90566884	3740009.19379795	3292251.66531919	2310688.79492013	4404239.59008605	3043289.12780863	825736.467181043	2523241.91730649	NA	474901.604069803	0	2955990.64049134	1917716.3427982	1767962.67737699	5926203.40397675	1639065.69474684	346810.763557826	1054776.22313737	2390258.27543894	1831346.37315857	1026696.36904362	7079792.50047866	4368341.01359769	3495986.87280275
--- a/tests/transformation_tests.R	Fri Jul 29 12:11:01 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,142 +0,0 @@
-library(RUnit)
-
-wrapperF <- function(argVc) {
-
-        source("../transformation_script.R")
-
-
-#### Start_of_testing_code <- function() {}
-
-
-##------------------------------
-## Initializing
-##------------------------------
-
-## options
-##--------
-
-strAsFacL <- options()[["stringsAsFactors"]]
-options(stringsAsFactors=FALSE)
-
-## constants
-##----------
-
-modNamC <- "Transformation" ## module name
-metVc <- c("log2", "log10") ## available methods
-
-topEnvC <- environment()
-flagC <- "\n"
-
-## functions
-##----------
-
-flgF <- function(tesC,
-                 envC = topEnvC,
-                 txtC = NA) { ## management of warning and error messages
-
-    tesL <- eval(parse(text = tesC), envir = envC)
-
-    if(!tesL) {
-
-        sink(NULL)
-        stpTxtC <- ifelse(is.na(txtC),
-                          paste0(tesC, " is FALSE"),
-                          txtC)
-
-        stop(stpTxtC,
-             call. = FALSE)
-
-    }
-
-} ## flgF
-
-## log file
-##---------
-
-sink(argVc[["information"]])
-
-cat("\nStart of the '", modNamC, "' module: ",
-    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
-
-## loading
-##--------
-
-datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]],
-                                check.names = FALSE,
-                                header = TRUE,
-                                row.names = 1,
-                                sep = "\t")))
-
-metC <- argVc[["method"]]
-
-## checking
-##---------
-
-flgF("metC %in% metVc", txtC = paste0("Transformation method must be either '", paste(metVc, collapse = "', '"), "'"))
-
-
-##------------------------------
-## Computation
-##------------------------------
-
-
-datMN <- transformF(datMN = datMN, ## dataMatrix
-                    metC = metC)  ## transformation method
-
-
-##------------------------------
-## Ending
-##------------------------------
-
-
-## saving
-##-------
-
-datDF <- cbind.data.frame(dataMatrix = colnames(datMN),
-                          as.data.frame(t(datMN)))
-write.table(datDF,
-            file = argVc[["dataMatrix_out"]],
-            quote = FALSE,
-            row.names = FALSE,
-            sep = "\t")
-
-## ending
-##-------
-
-cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
-    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
-
-sink()
-
-options(stringsAsFactors = strAsFacL)
-
-
-#### End_of_testing_code <- function() {}
-
-
-    return(list(datDF = datDF))
-
-    rm(list = ls())
-
-}
-
-exaDirOutC <- "output"
-file.exists(exaDirOutC) || dir.create(exaDirOutC)
-
-tesArgLs <- list(input_log10 = c(method = "log10",
-                     .chkC = "checkEqualsNumeric(outLs[['datDF']]['HMDB03072', 'HU_021'], 4.817089, tolerance = 1e-6)"))
-
-for(tesC in names(tesArgLs))
-    tesArgLs[[tesC]] <- c(tesArgLs[[tesC]],
-                          dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"),
-                          dataMatrix_out = file.path(exaDirOutC, "dataMatrix.tsv"),
-                          information = file.path(exaDirOutC, "information.txt"))
-
-for(tesC in names(tesArgLs)) {
-    print(tesC)
-    outLs <- wrapperF(tesArgLs[[tesC]])
-    if(".chkC" %in% names(tesArgLs[[tesC]]))
-        stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]])))
-}
-
-message("Checks successfully completed")
--- a/transformation_config.xml	Fri Jul 29 12:11:01 2016 -0400
+++ b/transformation_config.xml	Sat Aug 06 12:02:52 2016 -0400
@@ -1,93 +1,98 @@
-<tool id="Transformation" name="Transformation" version="2.0.2; 2016-07-27">
-	<description>Transforms the dataMatrix intensity values</description>
-
-	<requirements>
-	  <requirement type="package" version="3.2.2">R</requirement>
-	  <requirement type="package">r-batch</requirement>
-	</requirements>
-	
-	<command><![CDATA[
-	Rscript $__tool_directory__/transformation_wrapper.R
-			dataMatrix_in "$dataMatrix_in"
-			method "$method"
-			
-			dataMatrix_out "$dataMatrix_out"
-			information "$information"
-	]]></command>
+<tool id="Transformation" name="Transformation" version="2.2.0">
+  <description>Transforms the dataMatrix intensity values</description>
   
-	<inputs>
-		<param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
-		<param name="method" label="Method" type="select" help="">
-			<option value="log2">log2</option>
-			<option value="log10">log10</option>
-		</param>
-	</inputs>
+  <requirements>
+    <requirement type="package" version="3.2.2">R</requirement>
+    <requirement type="package">r-batch</requirement>
+  </requirements>
 
-	<outputs>
-		<data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
-		<data name="information" label="${tool.name}_information.txt" format="txt"/>
-	</outputs>
-	
-	<tests>
-	  <test>
-            <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
-            <param name="method" value="log10"/>
-            <output name="dataMatrix_out" file="output-dataMatrix.tsv"/>
-	  </test>
-	</tests>
-	
-	<help>
-
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+  
+  <command><![CDATA[
+  Rscript $__tool_directory__/transformation_wrapper.R
+  dataMatrix_in "$dataMatrix_in"
+  method "$method"
+  
+  dataMatrix_out "$dataMatrix_out"
+  information "$information"
+  ]]></command>
+  
+  <inputs>
+    <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
+    <param name="method" label="Method" type="select" help="">
+      <option value="log2">log2</option>
+      <option value="log10">log10</option>
+      <option value="sqrt">square root</option>
+    </param>
+  </inputs>
+  
+  <outputs>
+    <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
+    <data name="information" label="${tool.name}_information.txt" format="txt"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
+      <param name="method" value="log10"/>
+      <output name="dataMatrix_out" file="output-dataMatrix.tsv"/>
+    </test>
+  </tests>
+  
+  <help>
+    
 .. class:: infomark
-
+    
 **Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
-
+    
 ---------------------------------------------------
-
+    
 .. class:: infomark
-
+    
 **Tool updates**
-
+    
 See the **NEWS** section at the bottom of this page
-  
+    
 ---------------------------------------------------
-
+    
 ========================
 Transformation
 ========================
-
+    
 -----------
 Description
 -----------
-
- | Performs transformation of the dataMatrix intensity values aimed at stabilizing variance.
- | For mass spectrometry data, where multiplicative noise has been reported, logarithm transformation can be useful to make the peak intensity variance independent of the intensity mean (see for example Veselkov et al, 2011).
- | For the logarithm transformations, log(1+X) is used (to avoid returning -Inf for 0 values); NA values remain unchanged
- 
+    
+| Performs transformation of the dataMatrix intensity values aimed at stabilizing variance.
+| For mass spectrometry data, where multiplicative noise has been reported, logarithm transformation can be useful to make the peak intensity variance independent of the intensity mean (see for example Veselkov et al, 2011).
+| For the logarithm transformations, log(1+X) is used (to avoid returning -Inf for 0 values); NA values remain unchanged
+    
 | `Veselkov et al (2011). Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery. Analytical Chemistry, 83:5864-5872. &lt;http://dx.doi.org/10.1021/ac201065j&gt;`_
-
+    
 -----------------
 Workflow position
 -----------------
-
+    
 | In the workflow example below, the intensities are first transformed, before the signal drift and batch-effects are corrected; finally, the data quality is evaluated numerically and visually.
 |
-
+    
 .. image:: transformation_workflowPositionImage.png
-        :width: 600
-
-
-
+:width: 600
+    
+    
+    
 -----------
 Input files
 -----------
-
+    
 +----------------------------+---------+
 | Parameter : num + label    |  Format |
 +============================+=========+
 | 1 : Data matrix file       | tabular |
 +----------------------------+---------+
-
+    
 |
 | **Required format for the dataMatrix is described in the HowTo entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org**
 |
@@ -95,82 +100,92 @@
 ----------
 Parameters
 ----------
-	  
+    
 Method
-	| Method to be used for transforming the intensity values of the dataMatrix:
-	| **log2** (resp. **log10**): intensities values are log2 (resp. log10) transformed: log(1+X) is used to avoid generating -Inf for 0 values
-	| in case of negative intensities in the initial dataMatrix, an error is returned
-	| in case of missing (NA) intensities in the initial dataMatrix, these intensities remain set to NA after transformation
-
+| Method to be used for transforming the intensity values of the dataMatrix:
+| **log2** (resp. **log10**): intensities values are log2 (resp. log10) transformed: log(1+X) is used to avoid generating -Inf for 0 values
+| in case of negative intensities in the initial dataMatrix, an error is returned
+| in case of missing (NA) intensities in the initial dataMatrix, these intensities remain set to NA after transformation
+    
 ------------
 Output files
 ------------
-
+    
 dataMatrix_out.tabular
-	| dataMatrix data file with the transformed intensity values
-	| 
+| dataMatrix data file with the transformed intensity values
+| 
 
 information.txt
-	| Text file giving some informations about the computation (eg, number of NA and 0 values in the initial dataMatrix)
-	|
-
+| Text file giving some informations about the computation (eg, number of NA and 0 valuesin the initial dataMatrix)
+|
+    
 ---------------------------------------------------
-
+    
 ---------------
 Working example
 ---------------
-
+    
 .. class:: infomark
-
-See the **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu
-
+    
+See the **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
+    
 ---------------------------------------------------
-
+    
 ----
 NEWS
 ----
 
-CHANGES IN VERSION 2.0.2
+CHANGES IN VERSION 2.2.0
 ========================
 
+NEW FEATURE
+
+Square root transformation now available
+    
+CHANGES IN VERSION 2.0.2
+========================
+    
 INTERNAL MODIFICATIONS
-
+    
 Creating tests for R code
-
+    
   </help>
-
+  
   <citations>
     <citation type="bibtex">@Article{Thevenot2015,
-  Title                    = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
-  Author                   = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe},
-  Journal                  = {Journal of Proteome Research},
-  Year                     = {2015},
-  Note                     = {PMID: 26088811},
-  Number                   = {8},
-  Pages                    = {3322-3335},
-  Volume                   = {14},
+    Title                    = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
+    Author                   = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe},
+    Journal                  = {Journal of Proteome Research},
+    Year                     = {2015},
+    Note                     = {PMID: 26088811},
+    Number                   = {8},
+    Pages                    = {3322-3335},
+    Volume                   = {14},
+    
+    Doi                      = {10.1021/acs.jproteome.5b00354},
+    Url                      = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
+    }</citation>
+    <citation type="doi">10.1093/bioinformatics/btu813</citation>
+  </citations>
 
-  Doi                      = {10.1021/acs.jproteome.5b00354},
-  Url                      = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
-}</citation>
-
-</citations>
+  <!--
   
-Input files
-===========
+  Input files
+  ===========
+  
+  | **To generate the "dataMatrix":**
+  |   **1) copy/paste the values below in a .txt files**
+  |   **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
+  |     **Set the option 'Convert spaces to tabs' to 'Yes'**
+  | 
+  
+  **dataMatrix file**::
+  
+  dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209
+  HMDB01032 2569204.92420381 0 NA 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 NA 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586
+  HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 0 8932005.5351622 8340827.52597275 NA 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067
+  HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 NA 474901.604069803 0 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275
 
-| **To generate the "dataMatrix":**
-|   **1) copy/paste the values below in a .txt files**
-|   **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
-|     **Set the option 'Convert spaces to tabs' to 'Yes'**
-| 
-
-**dataMatrix file**::
-
-	dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209
-	HMDB01032 2569204.92420381 0 NA 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 NA 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586
-	HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 0 8932005.5351622 8340827.52597275 NA 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067
-	HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 NA 474901.604069803 0 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275
-
+-->
   
 </tool>
--- a/transformation_script.R	Fri Jul 29 12:11:01 2016 -0400
+++ b/transformation_script.R	Sat Aug 06 12:02:52 2016 -0400
@@ -5,42 +5,45 @@
 
 transformF <- function(datMN,
                        metC) {
-
+    
     ## options
-
+    
     optStrAsFacL <- options()[["stringsAsFactors"]]
     options(stringsAsFactors = FALSE)
-
+    
+    ## checking		     
+    
+    if(length(which(datMN < 0))) {
+        cat("\nThe 'dataMatrix' contains negative values\n")
+        sink()
+        stop("The 'dataMatrix' contains negative values", call. = FALSE)
+    }
+    
+    ## Number of missing values
+    nasN <- length(which(is.na(datMN)))
+    cat("\nMissing values in the 'dataMatrix': ",
+        nasN,
+        " (",
+        round(nasN / cumprod(dim(datMN))[2] * 100),
+        "%)\n",
+        sep="")
+    
+    ## Number of zero values
+    zerN <- length(which(datMN == 0))
+    cat("\nZero values in the 'dataMatrix': ",
+        zerN,
+        " (",
+        round(zerN / cumprod(dim(datMN))[2] * 100),
+        "%)\n",
+        sep="")
+    
     ## transformation
-
+    
     switch(metC,
            log2 = {
 
                cat("\n'log2' transformation\n", sep="")
 
-               if(length(which(datMN < 0)))
-                   stop("The 'dataMatrix' contains negative values")
-
-               zerMN <- datMN == 0
-
-               ## Number of missing values
-               nasN <- length(which(is.na(datMN)))
-               cat("\nMissing values in the 'dataMatrix': ",
-                   nasN,
-                   " (",
-                   round(nasN / cumprod(dim(datMN))[2] * 100),
-                   "%)\n",
-                   sep="")
-
-               ## Number of zero values
-               zerN <- length(which(zerMN))
-               cat("\nZero values in the 'dataMatrix': ",
-                   zerN,
-                   " (",
-                   round(zerN / cumprod(dim(datMN))[2] * 100),
-                   "%)\n",
-                   sep="")
-
                trfMN <- log2(1 + datMN)
 
            },
@@ -48,32 +51,17 @@
 
                cat("\n'log10' transformation\n", sep="")
 
-               if(length(which(datMN < 0)))
-                   stop("The 'dataMatrix' contains negative values")
-
-               zerMN <- datMN == 0
-
-               ## Number of missing values
-               nasN <- length(which(is.na(datMN)))
-               cat("\nMissing values in the 'dataMatrix': ",
-                   nasN,
-                   " (",
-                   round(nasN / cumprod(dim(datMN))[2] * 100),
-                   "%)\n",
-                   sep="")
-
-               ## Number of zero values
-               zerN <- length(which(zerMN))
-               cat("\nZero values in the 'dataMatrix': ",
-                   zerN,
-                   " (",
-                   round(zerN / cumprod(dim(datMN))[2] * 100),
-                   "%)\n",
-                   sep="")
-
                trfMN <- log10(1 + datMN)
 
-           }) ## end of 'log10' method
+           },
+           sqrt = {
+
+               cat("\n'Square root' transformation\n", sep="")
+               
+               trfMN <- sqrt(datMN)
+
+
+           }) ## end of method
 
 
     ## returning
--- a/transformation_wrapper.R	Fri Jul 29 12:11:01 2016 -0400
+++ b/transformation_wrapper.R	Sat Aug 06 12:02:52 2016 -0400
@@ -1,5 +1,4 @@
-#!/usr/bin/Rscript --vanilla --slave --no-site-file
-
+#!/usr/bin/env Rscript
 
 library(batch) ## parseCommandArgs
 
@@ -14,9 +13,6 @@
 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
 
 
-#### Start_of_tested_code  <- function() {}
-
-
 ##------------------------------
 ## Initializing
 ##------------------------------
@@ -31,33 +27,7 @@
 ##----------
 
 modNamC <- "Transformation" ## module name
-metVc <- c("log2", "log10") ## available methods
 
-topEnvC <- environment()
-flagC <- "\n"
-
-## functions
-##----------
-
-flgF <- function(tesC,
-                 envC = topEnvC,
-                 txtC = NA) { ## management of warning and error messages
-
-    tesL <- eval(parse(text = tesC), envir = envC)
-
-    if(!tesL) {
-
-        sink(NULL)
-        stpTxtC <- ifelse(is.na(txtC),
-                          paste0(tesC, " is FALSE"),
-                          txtC)
-
-        stop(stpTxtC,
-             call. = FALSE)
-
-    }
-
-} ## flgF
 
 ## log file
 ##---------
@@ -78,11 +48,6 @@
 
 metC <- argVc[["method"]]
 
-## checking
-##---------
-
-flgF("metC %in% metVc", txtC = paste0("Transformation method must be either '", paste(metVc, collapse = "', '"), "'"))
-
 
 ##------------------------------
 ## Computation
@@ -120,7 +85,4 @@
 options(stringsAsFactors = strAsFacL)
 
 
-#### End_of_tested_code <- function() {}
-
-
 rm(list = ls())