Mercurial > repos > ethevenot > univariate

changeset 2:09799fc16bc6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
author ethevenot
date Sat, 06 Aug 2016 12:42:42 -0400
parents fdefbc780d2e
children 140290de7986
files README.md docker/Dockerfile runit/example1/dataMatrix.tsv runit/example1/sampleMetadata.tsv runit/example1/variableMetadata.tsv runit/input/dataMatrix.tsv runit/input/sampleMetadata.tsv runit/input/variableMetadata.tsv runit/output/information.txt runit/output/variableMetadata.tsv runit/univariate_runtests.R runit/univariate_tests.R test-data/output-variableMetadata.tsv test-data/variableMetadata-output.tsv tests/example1/dataMatrix.tsv tests/example1/sampleMetadata.tsv tests/example1/variableMetadata.tsv tests/input/dataMatrix.tsv tests/input/sampleMetadata.tsv tests/input/variableMetadata.tsv tests/output/information.txt tests/output/variableMetadata.tsv tests/univariate_tests.R univariate_config.xml univariate_script.R univariate_wrapper.R
diffstat 26 files changed, 399 insertions(+), 394 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Sat Jul 30 12:38:02 2016 -0400
+++ b/README.md	Sat Aug 06 12:42:42 2016 -0400
@@ -1,13 +1,14 @@
-# Univariate parametric and non-parametric hypothesis testing with correction for multiple testing
+Univariate parametric and non-parametric hypothesis testing with correction for multiple testing  
+================================================================================================  
 
-A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project.
+A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure    
 
 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/univariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/univariate).
 
-## Description
+### Description
 
-**Version:** 2.1.2   
-**Date:** 2016-07-30  
+**Version:** 2.1.4   
+**Date:** 2016-08-05  
 **Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)    
 **Email:** [marie.tremblay-franco(at)toulouse.inra.fr](mailto:marie.tremblay-franco@toulouse.inra.fr); [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)  
@@ -15,27 +16,58 @@
 **Licence:** CeCILL  
 **Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)
 
-## Installation
+### Installation
 
- * Configuration file: **univariate_config.xml**  
+ * Configuration file: `univariate_config.xml`  
  * Image file: 
-  + **static/images/univariate_workflowPositionImage.png**   
- * Wrapper file: **univariate_wrapper.R**  
- * Script file: **univariate_script.R**  
+  + `static/images/univariate_workflowPositionImage.png`   
+ * Wrapper file: `univariate_wrapper.R`  
+ * Script file: `univariate_script.R`  
  * R packages  
-  + **batch** from CRAN: `install.packages("batch", dep=TRUE)`.
-  + **PMCMR** from Bioconductor: `install.packages("PMCMR", dep=TRUE)`.
+  + **batch** from CRAN  
+  
+    ```r
+    install.packages("batch", dep=TRUE)  
+    ```
+  + **PMCMR** from CRAN  
+  
+    ```r  
+    install.packages("PMCMR", dep=TRUE)  
+    ```    
+ 
+### Tests
 
-## Tests
+The code in the wrapper can be tested by running the `runit/univariate_runtests.R` R file
+
+You will need to install **RUnit** package in order to make it run:
+```r
+install.packages('RUnit', dependencies = TRUE)
+```
 
-The code in the wrapper can be tested by running the **tests/univariate_tests.R** in R  
+### Working example  
+
+See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)  
+
+### News
+
+###### CHANGES IN VERSION 2.1.4
+
+NEW FEATURE  
 
-## News
+Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously)  
+
+INTERNAL MODIFICATION  
 
-## CHANGES IN VERSION 2.1.2  
+ * Minor internal changes  
+
+###### CHANGES IN VERSION 2.1.2  
+
+INTERNAL MODIFICATION  
 
  * Minor internal changes in .shed.yml for toolshed export
 
-## CHANGES IN VERSION 2.1.1  
+###### CHANGES IN VERSION 2.1.1  
+
+INTERNAL MODIFICATION  
 
  * Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples).
--- a/docker/Dockerfile	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-FROM ubuntu:14.04
-
-MAINTAINER Etienne Thevenot (etienne.thevenot@cea.fr)
-
-# Setup package repos
-RUN echo "deb http://mirrors.ebi.ac.uk/CRAN/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list
-RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
-
-# Update and upgrade system
-RUN apt-get update
-RUN apt-get -y upgrade
-
-# Install R and other needed packages
-RUN apt-get -y install r-base
-RUN R -e "install.packages('batch', lib='/usr/lib/R/library', dependencies = TRUE, repos='http://mirrors.ebi.ac.uk/CRAN')"
-
-# Clone tool
-RUN apt-get -y install git
-RUN git clone -b docker https://github.com/workflow4metabolomics/univariate /files/univariate
-
-# Put univariate folder into PATH
-ENV PATH=$PATH:/files/univariate
-
-# Clean up
-RUN apt-get clean && apt-get autoremove -y && rm -rf /var/lib/{apt,dpkg,cache,log}/ /tmp/* /var/tmp/*
-
-# Define Entry point script
-ENTRYPOINT ["/files/univariate/univariate_wrapper.R"]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/example1/dataMatrix.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,4 @@
+dataMatrix	Ech10	Ech11	Ech12	Ech13	Ech14	Ech15
+MT1	3.439956551	3.399847335	3.335401704	3.4201777	3.24585851	3.401256321
+MT2	5.008458405	4.461291924	4.068043169	4.42768414	4.406640829	4.500370048
+MT3	3.99527636	4.051758488	4.332552332	4.348474118	4.253679544	4.26823853
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/example1/sampleMetadata.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,7 @@
+sampleMetadata	jour
+Ech10	J10
+Ech11	J10
+Ech12	J10
+Ech13	J3
+Ech14	J3
+Ech15	J3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/example1/variableMetadata.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,4 @@
+variableMetadata	PCA_XLOAD-h1	PCA_XLOAD-h2
+MT1	-0.048723936	0.05648187
+MT2	-0.067609139	0.084300327
+MT3	0.080335733	-0.0215397
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/dataMatrix.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,4 @@
+profile	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	6222035.77434915	17070707.9912636	1258838.24348419	13039543.0754619	1909391.77026598	3495.09386434063	2293521.90928998	128503.275117713	81872.5276382213	8103557.56578035	149574887.036181	1544036.41049333	7103429.53933206	14138796.50382	4970265.57952158	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	3260583.81592376	8932005.5351622	8340827.52597275	9256460.69197759	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	6030501.02648005	474901.604069803	2885792.42617652	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/input/sampleMetadata.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,31 @@
+sample	age	ageGroup
+HU_017	41	experienced
+HU_021	34	junior
+HU_027	37	experienced
+HU_032	38	experienced
+HU_041	28	junior
+HU_048	39	experienced
+HU_049	50	senior
+HU_050	30	junior
+HU_052	51	senior
+HU_059	81	senior
+HU_060	55	senior
+HU_066	25	junior
+HU_072	47	experienced
+HU_077	27	junior
+HU_090	46	experienced
+HU_109	32	junior
+HU_110	50	senior
+HU_125	58	senior
+HU_126	45	experienced
+HU_131	42	experienced
+HU_134	48	experienced
+HU_149	35	experienced
+HU_150	49	experienced
+HU_173	55	senior
+HU_179	33	junior
+HU_180	53	senior
+HU_182	43	experienced
+HU_202	42	experienced
+HU_204	31	junior
+HU_209	17.5	junior
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/variableMetadata.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,4 @@
+variable	name
+HMDB01032	Dehydroepiandrosterone sulfate
+HMDB03072	Quinic acid
+HMDB00792	Sebacic acid
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/information.txt	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,9 @@
+
+Start of the 'Univariate' Galaxy module call: Sat 06 Aug 2016 06:22:18 PM
+
+Performing 'kruskal'
+
+The following 1 variable (33%) was found significant at the 0.05 level:
+HMDB01032
+
+End of 'Univariate' Galaxy module call: 2016-08-06 18:22:18
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/variableMetadata.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,4 @@
+variableMetadata	name	ageGroup_kruskal_fdr	ageGroup_kruskal_sig	ageGroup_kruskal_junior.experienced_dif	ageGroup_kruskal_senior.experienced_dif	ageGroup_kruskal_senior.junior_dif	ageGroup_kruskal_junior.experienced_pva	ageGroup_kruskal_senior.experienced_pva	ageGroup_kruskal_senior.junior_pva	ageGroup_kruskal_junior.experienced_sig	ageGroup_kruskal_senior.experienced_sig	ageGroup_kruskal_senior.junior_sig
+HMDB01032	Dehydroepiandrosterone sulfate	0.0117826825222329	1	7211389.71960377	-1703486.11807139	-8914875.83767516	0.204550960009346	0.123124593762726	0.00251932966039092	0	0	1
+HMDB03072	Quinic acid	0.461634758626427	0	-3747468.87812489	1512795.66143568	5260264.53956057	NA	NA	NA	NA	NA	NA
+HMDB00792	Sebacic acid	0.469555338459932	0	1404223.43306179	959174.915801485	-445048.517260305	NA	NA	NA	NA	NA	NA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/univariate_runtests.R	Sat Aug 06 12:42:42 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), "..", "univariate_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 univariate_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[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.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)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/univariate_tests.R	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,44 @@
+test_input_kruskal <- function() {
+
+    testDirC <- "input"
+    argLs <- list(facC = "ageGroup",
+                  tesC = "kruskal",
+                  adjC = "fdr",
+                  thrN = "0.05")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+
+    checkEqualsNumeric(outLs[["varDF"]]["HMDB01032", "ageGroup_kruskal_senior.experienced_pva"], 0.1231246, tolerance = 1e-6)
+
+}
+
+test_example1_wilcoxDif <- function() {
+
+    testDirC <- "example1"
+    argLs <- list(facC = "jour",
+                  tesC = "wilcoxon",
+                  adjC = "fdr",
+                  thrN = "0.05")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+    
+    checkEqualsNumeric(outLs[["varDF"]]["MT3", "jour_wilcoxon_J3.J10_dif"], 0.216480042, tolerance = 1e-8)
+
+}
+
+test_example1_ttestFdr <- function() {
+
+    testDirC <- "example1"
+    argLs <- list(facC = "jour",
+                  tesC = "ttest",
+                  adjC = "fdr",
+                  thrN = "0.05")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+
+    checkEqualsNumeric(outLs[["varDF"]]["MT3", "jour_ttest_J3.J10_fdr"], 0.7605966, tolerance = 1e-6)
+
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output-variableMetadata.tsv	Sat Aug 06 12:42:42 2016 -0400
@@ -0,0 +1,4 @@
+variableMetadata	name	ageGroup_kruskal_fdr	ageGroup_kruskal_sig	ageGroup_kruskal_junior.experienced_dif	ageGroup_kruskal_senior.experienced_dif	ageGroup_kruskal_senior.junior_dif	ageGroup_kruskal_junior.experienced_pva	ageGroup_kruskal_senior.experienced_pva	ageGroup_kruskal_senior.junior_pva	ageGroup_kruskal_junior.experienced_sig	ageGroup_kruskal_senior.experienced_sig	ageGroup_kruskal_senior.junior_sig
+HMDB01032	Dehydroepiandrosterone sulfate	0.0117826825222329	1	7211389.71960377	-1703486.11807139	-8914875.83767516	0.204550960009346	0.123124593762726	0.00251932966039092	0	0	1
+HMDB03072	Quinic acid	0.461634758626427	0	-3747468.87812489	1512795.66143568	5260264.53956057	NA	NA	NA	NA	NA	NA
+HMDB00792	Sebacic acid	0.469555338459932	0	1404223.43306179	959174.915801485	-445048.517260305	NA	NA	NA	NA	NA	NA
--- a/test-data/variableMetadata-output.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-variableMetadata	name	ageGroup_kruskal_fdr	ageGroup_kruskal_sig	ageGroup_kruskal_junior-experienced_dif	ageGroup_kruskal_senior-experienced_dif	ageGroup_kruskal_senior-junior_dif	ageGroup_kruskal_junior-experienced_pva	ageGroup_kruskal_senior-experienced_pva	ageGroup_kruskal_senior-junior_pva	ageGroup_kruskal_junior-experienced_sig	ageGroup_kruskal_senior-experienced_sig	ageGroup_kruskal_senior-junior_sig
-HMDB01032	Dehydroepiandrosterone sulfate	0.0117826825222329	1	7211389.71960377	-1703486.11807139	-8914875.83767516	0.204550960009346	0.123124593762726	0.00251932966039092	0	0	1
-HMDB03072	Quinic acid	0.461634758626427	0	-3747468.87812489	1512795.66143568	5260264.53956057	NA	NA	NA	NA	NA	NA
-HMDB00792	Sebacic acid	0.469555338459932	0	1404223.43306179	959174.915801485	-445048.517260305	NA	NA	NA	NA	NA	NA
--- a/tests/example1/dataMatrix.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-dataMatrix	Ech10	Ech11	Ech12	Ech13	Ech14	Ech15
-MT1	3.439956551	3.399847335	3.335401704	3.4201777	3.24585851	3.401256321
-MT2	5.008458405	4.461291924	4.068043169	4.42768414	4.406640829	4.500370048
-MT3	3.99527636	4.051758488	4.332552332	4.348474118	4.253679544	4.26823853
--- a/tests/example1/sampleMetadata.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-sampleMetadata	jour
-Ech10	J10
-Ech11	J10
-Ech12	J10
-Ech13	J3
-Ech14	J3
-Ech15	J3
--- a/tests/example1/variableMetadata.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-variableMetadata	PCA_XLOAD-h1	PCA_XLOAD-h2
-MT1	-0.048723936	0.05648187
-MT2	-0.067609139	0.084300327
-MT3	0.080335733	-0.0215397
--- a/tests/input/dataMatrix.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-profile	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	6222035.77434915	17070707.9912636	1258838.24348419	13039543.0754619	1909391.77026598	3495.09386434063	2293521.90928998	128503.275117713	81872.5276382213	8103557.56578035	149574887.036181	1544036.41049333	7103429.53933206	14138796.50382	4970265.57952158	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	3260583.81592376	8932005.5351622	8340827.52597275	9256460.69197759	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	6030501.02648005	474901.604069803	2885792.42617652	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/input/sampleMetadata.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-sample	age	ageGroup
-HU_017	41	experienced
-HU_021	34	junior
-HU_027	37	experienced
-HU_032	38	experienced
-HU_041	28	junior
-HU_048	39	experienced
-HU_049	50	senior
-HU_050	30	junior
-HU_052	51	senior
-HU_059	81	senior
-HU_060	55	senior
-HU_066	25	junior
-HU_072	47	experienced
-HU_077	27	junior
-HU_090	46	experienced
-HU_109	32	junior
-HU_110	50	senior
-HU_125	58	senior
-HU_126	45	experienced
-HU_131	42	experienced
-HU_134	48	experienced
-HU_149	35	experienced
-HU_150	49	experienced
-HU_173	55	senior
-HU_179	33	junior
-HU_180	53	senior
-HU_182	43	experienced
-HU_202	42	experienced
-HU_204	31	junior
-HU_209	17.5	junior
--- a/tests/input/variableMetadata.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-variable	name
-HMDB01032	Dehydroepiandrosterone sulfate
-HMDB03072	Quinic acid
-HMDB00792	Sebacic acid
--- a/tests/output/information.txt	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-
-Start of the 'Univariate' Galaxy module call: sam. 21 mai 2016 20:25:53
-
-Performing 'ttest'
-
-No significant variable found at the selected 0.05 level
-
-End of 'Univariate' Galaxy module call: 2016-05-21 20:25:53
--- a/tests/output/variableMetadata.tsv	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-variableMetadata	PCA_XLOAD-h1	PCA_XLOAD-h2	jour_ttest_J3-J10_dif	jour_ttest_J3-J10_fdr	jour_ttest_J3-J10_sig
-MT1	-0.048723936	0.05648187	-0.0359710196666665	0.827558403950534	0
-MT2	-0.067609139	0.084300327	-0.0676994936666668	0.827558403950534	0
-MT3	0.080335733	-0.0215397	0.163601670666666	0.760596565270778	0
--- a/tests/univariate_tests.R	Sat Jul 30 12:38:02 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,194 +0,0 @@
-library(RUnit)
-
-wrapperF <- function(argVc) {
-
-
-    source("../univariate_script.R")
-
-
-#### Start_of_testing_code <- function() {}
-
-
-    ##------------------------------
-    ## Initializing
-    ##------------------------------
-
-    ## options
-    ##--------
-
-    strAsFacL <- options()$stringsAsFactors
-    options(stringsAsFactors = FALSE)
-
-    ## packages
-    ##---------
-
-    library(PMCMR)
-
-    ## constants
-    ##----------
-
-    modNamC <- "Univariate" ## module name
-
-    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, "' Galaxy module call: ",
-        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")))
-
-    samDF <- read.table(argVc["sampleMetadata_in"],
-                        check.names = FALSE,
-                        header = TRUE,
-                        row.names = 1,
-                        sep = "\t")
-
-    varDF <- read.table(argVc["variableMetadata_in"],
-                        check.names = FALSE,
-                        header = TRUE,
-                        row.names = 1,
-                        sep = "\t")
-
-    tesC <- argVc["tesC"]
-
-    ## checking
-    ##---------
-
-    flgF("identical(rownames(datMN), rownames(samDF))", txtC = "Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
-    flgF("identical(colnames(datMN), rownames(varDF))", txtC = "Row names of the dataMatrix are not identical to the row names of the variableMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
-
-    flgF("argVc['facC'] %in% colnames(samDF)", txtC = paste0("Required factor of interest '", argVc['facC'], "' could not be found in the column names of the sampleMetadata"))
-    flgF("mode(samDF[, argVc['facC']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc['facC'], "' column of the sampleMetadata should contain either number only, or character only"))
-
-    flgF("!(tesC %in% c('ttest', 'wilcoxon')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) == 2)", txtC = paste0("For 'ttest' and 'wilcoxon', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with only two different classes"))
-    flgF("!(tesC %in% c('anova', 'kruskal')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) > 2)", txtC = paste0("For 'anova' and 'kruskal', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with at least three different classes"))
-    flgF("!(tesC %in% c('pearson', 'spearman')) || mode(samDF[, argVc['facC']]) == 'numeric'", txtC = paste0("For 'pearson' and 'spearman', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain numbers only"))
-
-    flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')")
-
-    flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1",
-         txtC = "(corrected) p-value threshold must be between 0 and 1")
-
-
-    ##------------------------------
-    ## Computation
-    ##------------------------------
-
-
-    varDF <- univariateF(datMN = datMN,
-                         samDF = samDF,
-                         varDF = varDF,
-                         facC = argVc["facC"],
-                         tesC = tesC,
-                         adjC = argVc["adjC"],
-                         thrN = as.numeric(argVc["thrN"]))
-
-
-    ##------------------------------
-    ## Ending
-    ##------------------------------
-
-
-    ## saving
-    ##--------
-
-    varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
-                              varDF)
-    write.table(varDF,
-                file = argVc["variableMetadata_out"],
-                quote = FALSE,
-                row.names = FALSE,
-                sep = "\t")
-
-    ## closing
-    ##--------
-
-    cat("\nEnd of '", modNamC, "' Galaxy module call: ",
-        as.character(Sys.time()), "\n", sep = "")
-
-    sink()
-
-    options(stringsAsFactors = strAsFacL)
-
-
-
-#### End_of_testing_code <- function() {}
-
-
-    return(list(varDF = varDF))
-
-    rm(list = ls())
-
-}
-
-exaDirOutC <- "output"
-if(!file.exists(exaDirOutC))
-   stop("Please create an 'output' subfolder into the (current) 'tests' folder")
-
-tesArgLs <- list(input_kruskal = c(facC = "ageGroup",
-                     tesC = "kruskal",
-                     adjC = "fdr",
-                     thrN = "0.05",
-                     .chkC = "checkEqualsNumeric(outLs[['varDF']]['HMDB01032', 'ageGroup_kruskal_senior-experienced_pva'], 0.1231246, tolerance = 1e-6)"),
-                 example1_wilcoxDif = c(facC = "jour",
-                     tesC = "wilcoxon",
-                     adjC = "fdr",
-                     thrN = "0.05",
-                     .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_wilcoxon_J3-J10_dif'], 0.216480042, tolerance = 1e-8)"),
-                 example1_ttestFdr = c(facC = "jour",
-                     tesC = "ttest",
-                     adjC = "fdr",
-                     thrN = "0.05",
-                     .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_ttest_J3-J10_fdr'], 0.7605966, tolerance = 1e-6)"))
-
-for(tesC in names(tesArgLs))
-    tesArgLs[[tesC]] <- c(tesArgLs[[tesC]],
-                          dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"),
-                          sampleMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "sampleMetadata.tsv"),
-                          variableMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "variableMetadata.tsv"),
-                          variableMetadata_out = file.path(exaDirOutC, "variableMetadata.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/univariate_config.xml	Sat Jul 30 12:38:02 2016 -0400
+++ b/univariate_config.xml	Sat Aug 06 12:42:42 2016 -0400
@@ -1,71 +1,75 @@
-<tool id="Univariate" name="Univariate" version="2.1.2">
+<tool id="Univariate" name="Univariate" version="2.1.4">
   <description>Univariate statistics</description>
+  
+  <requirements>
+    <requirement type="package" version="3.2.2">R</requirement>
+    <requirement type="package">r-batch</requirement>
+    <requirement type="package">r-PMCMR</requirement>
+  </requirements>
 
-	<requirements>
-		<requirement type="package" version="3.2.2">R</requirement>
-		<requirement type="package">r-batch</requirement>
-		<requirement type="package">r-pmcmr</requirement>
-	</requirements>
-
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+  
   <command><![CDATA[
-	  $__tool_directory__/univariate_wrapper.R
-      dataMatrix_in "$dataMatrix_in"
-      sampleMetadata_in "$sampleMetadata_in"
-      variableMetadata_in "$variableMetadata_in"
+  Rscript $__tool_directory__/univariate_wrapper.R
 
-	  facC "$facC"
-	  tesC "$tesC"
-	  adjC "$adjC"
-	  thrN "$thrN"	  
-
-      variableMetadata_out "$variableMetadata_out"
-	  information "$information"
+  dataMatrix_in "$dataMatrix_in"
+  sampleMetadata_in "$sampleMetadata_in"
+  variableMetadata_in "$variableMetadata_in"
+  
+  facC "$facC"
+  tesC "$tesC"
+  adjC "$adjC"
+  thrN "$thrN"	  
+  
+  variableMetadata_out "$variableMetadata_out"
+  information "$information"
   ]]></command>
-
   <inputs>
-	<param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
-	<param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
-	<param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular"  />
+    <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
+    <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
+    <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular"  />
     <param name="facC" label="Factor of interest" type="text" help="Name of the column of the sample metadata table corresponding to the qualitative or quantitative variable"/>
     <param name="tesC" label="Test" type="select" help="">
-		<option value="ttest">ttest (qualitative, 2 levels)</option>
-        <option value="wilcoxon">Wilcoxon test (qualitative, 2 levels)</option>      
-		<option value="anova">Analysis of variance (qualitative, more than 2 levels)</option>
-		<option value="kruskal">Kruskal-Wallis rank test (qualitative, more than 2 levels)</option>
-		<option value="pearson">Pearson correlation test (quantitative)</option>
-		<option value="spearman">Spearman correlation rank test (quantitative)</option>
+      <option value="ttest">ttest (qualitative, 2 levels)</option>
+      <option value="wilcoxon">Wilcoxon test (qualitative, 2 levels)</option>      
+      <option value="anova">Analysis of variance (qualitative, more than 2 levels)</option>
+      <option value="kruskal">Kruskal-Wallis rank test (qualitative, more than 2 levels)</option>
+      <option value="pearson">Pearson correlation test (quantitative)</option>
+      <option value="spearman">Spearman correlation rank test (quantitative)</option>
     </param>
     <param name="adjC" label="Method for multiple testing correction" type="select" help="">
-	    <option value="fdr">fdr</option>
-		<option value="BH">BH</option>
-		<option value="bonferroni">bonferroni</option>
-		<option value="BY">BY</option>
-		<option value="hochberg">hochberg</option>
-        <option value="holm">holm</option>
-		<option value="hommel">hommel</option>
-		<option value="none">none</option>
+      <option value="fdr">fdr</option>
+      <option value="BH">BH</option>
+      <option value="bonferroni">bonferroni</option>
+      <option value="BY">BY</option>
+      <option value="hochberg">hochberg</option>
+      <option value="holm">holm</option>
+      <option value="hommel">hommel</option>
+      <option value="none">none</option>
     </param>
     <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/>
-   </inputs>
-
+  </inputs>
+  
   <outputs>
     <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
-	<data name="information" label="${tool.name}_information.txt" format="txt"/>
+    <data name="information" label="${tool.name}_information.txt" format="txt"/>
   </outputs>
-
+  
   <tests>
-	  <test>
-		  <param name="dataMatrix_in" value="dataMatrix.tsv"/>
-		  <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>
-		  <param name="variableMetadata_in" value="variableMetadata.tsv"/>
-		  <param name="facC" value="ageGroup"/>
-		  <param name="tesC" value="kruskal"/>
-		  <param name="adjC" value="fdr"/>
-		  <param name="thrN" value="0.05"/>
-		  <output name="variableMetadata_out" file="variableMetadata-output.tsv"/>
-	  </test>
+    <test>
+      <param name="dataMatrix_in" value="dataMatrix.tsv"/>
+      <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>
+      <param name="variableMetadata_in" value="variableMetadata.tsv"/>
+      <param name="facC" value="ageGroup"/>
+      <param name="tesC" value="kruskal"/>
+      <param name="adjC" value="fdr"/>
+      <param name="thrN" value="0.05"/>
+      <output name="variableMetadata_out" file="output-variableMetadata.tsv"/>
+    </test>
   </tests>
-
+  
   <help>
 
 .. class:: infomark
@@ -200,6 +204,78 @@
 Working example
 ---------------
 
+.. class:: infomark
+
+See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
+
+---------------------------------------------------
+
+----
+NEWS
+----
+
+CHANGES IN VERSION 2.1.4
+========================
+
+NEW FEATURE
+
+Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously)
+
+INTERNAL MODIFICATIONS
+
+Minor internal changes for toolshed export
+
+CHANGES IN VERSION 2.1.2
+========================
+
+INTERNAL MODIFICATIONS
+
+Minor internal changes for toolshed export
+
+CHANGES IN VERSION 2.1.1
+========================
+
+INTERNAL MODIFICATIONS
+
+Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples)
+
+CHANGES IN VERSION 2.0.1
+========================
+
+NEW FEATURE
+
+(corrected) p-value threshold can be set to any value between 0 and 1
+
+
+</help>
+
+<citations>
+  <citation type="bibtex">@Manual{,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2016},
+  url = {https://www.R-project.org/},
+  }</citation>
+  <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                   = {Thevenot, Etienne A. and Roux, Aurelie 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>
+
+
+
 Input files
 ===========
 
@@ -291,28 +367,5 @@
 
 ---------------------------------------------------
 
-----
-NEWS
-----
-
-CHANGES IN VERSION 2.1.2
-========================
-
-Minor internal changes for toolshed export
-
-CHANGES IN VERSION 2.1.1
-========================
-
-Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples)
-
-CHANGES IN VERSION 2.0.1
-========================
-
-(corrected) p-value threshold can be set to any value between 0 and 1
-
-
-  </help>
-
-  <citations/>
 
 </tool>
--- a/univariate_script.R	Sat Jul 30 12:38:02 2016 -0400
+++ b/univariate_script.R	Sat Aug 06 12:42:42 2016 -0400
@@ -54,7 +54,7 @@
         sigVn <- as.numeric(fdrVn < thrN)
 
         if(tesC %in% c("ttest", "wilcoxon"))
-            varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "-"), "_")
+            varPfxC <- paste0(varPfxC, paste(rev(facLevVc), collapse = "."), "_")
 
         varDF[, paste0(varPfxC, ifelse(tesC %in% c("ttest", "wilcoxon"), "dif", "cor"))] <- staVn
 
@@ -67,6 +67,8 @@
         ## getting the names of the pairwise comparisons 'class1Vclass2'
         prwVc <- rownames(TukeyHSD(aov(datMN[, 1] ~ facFcVn))[["facFcVn"]])
 
+        prwVc <- gsub("-", ".", prwVc, fixed = TRUE) ## 2016-08-05: '-' character in dataframe column names seems not to be converted to "." by write.table on ubuntu R-3.3.1
+
         aovMN <- t(apply(datMN, 2, function(varVn) {
 
             aovMod <- aov(varVn ~ facFcVn)
@@ -97,9 +99,9 @@
         nemVl <- c(lower.tri(nemMN, diag = TRUE))
         nemClaMC <- cbind(rownames(nemMN)[c(row(nemMN))][nemVl],
                           colnames(nemMN)[c(col(nemMN))][nemVl])
-        nemNamVc <- paste0(nemClaMC[, 1], "-", nemClaMC[, 2])
+        nemNamVc <- paste0(nemClaMC[, 1], ".", nemClaMC[, 2])
         nemNamVc <- paste0(varPfxC, nemNamVc)
-
+        
         nemMN <- t(apply(datMN, 2, function(varVn) {
 
             pvaN <- kruskal.test(varVn ~ facFcVn)[["p.value"]]
--- a/univariate_wrapper.R	Sat Jul 30 12:38:02 2016 -0400
+++ b/univariate_wrapper.R	Sat Aug 06 12:42:42 2016 -0400
@@ -12,10 +12,6 @@
 
 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
 
-
-#### Start_of_tested_code  <- function() {}
-
-
 ##------------------------------
 ## Initializing
 ##------------------------------
@@ -136,6 +132,7 @@
 
 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
                           varDF)
+
 write.table(varDF,
             file = argVc["variableMetadata_out"],
             quote = FALSE,
@@ -152,8 +149,4 @@
 
 options(stringsAsFactors = strAsFacL)
 
-
-#### End_of_tested_code <- function() {}
-
-
 rm(list = ls())