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changeset 4:3017385625f6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
author ethevenot
date Thu, 11 Jan 2018 10:21:17 -0500
parents 140290de7986
children 5687435b182c
files Makefile README.md build.xml runit/output/figure.pdf runit/output/information.txt test/.gitignore test/test-univ univariate_config.xml univariate_wrapper.R
diffstat 9 files changed, 136 insertions(+), 115 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Thu Jan 11 10:21:17 2018 -0500
@@ -0,0 +1,23 @@
+all:
+
+test:
+	test/test-univ
+
+planemo-venv/bin/planemo: planemo-venv
+	. planemo-venv/bin/activate && pip install --upgrade pip setuptools
+	. planemo-venv/bin/activate && pip install planemo
+
+planemo-venv:
+	virtualenv planemo-venv
+
+planemolint: planemo-venv/bin/planemo
+	. planemo-venv/bin/activate && planemo lint
+
+planemotest: planemo-venv/bin/planemo
+	. planemo-venv/bin/activate && planemo test --conda_dependency_resolution --galaxy_branch release_17.05
+
+clean:
+	$(RM) -r $(HOME)/.planemo
+	$(RM) -r planemo-venv
+
+.PHONY:	all clean test planemolint planemotest
--- a/README.md	Sun Oct 30 14:17:09 2016 -0400
+++ b/README.md	Thu Jan 11 10:21:17 2018 -0500
@@ -7,8 +7,8 @@
 
 ### Description
 
-**Version:** 2.2.0   
-**Date:** 2016-10-30  
+**Version:** 2.2.4   
+**Date:** 2018-01-11  
 **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)  
@@ -50,6 +50,12 @@
 
 ### News
 
+###### CHANGES IN VERSION 2.2.4  
+
+MINOR MODIFICATION  
+
+ * Internal minor modifications for building and testing  
+
 ###### CHANGES IN VERSION 2.2.0  
 
 MAJOR MODIFICATION  
--- a/build.xml	Sun Oct 30 14:17:09 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-<project name="w4m.univariate" default="all">
-
-	<property name="tool.xml" value="univariate_config.xml"/>
-	<property name="conda.dir" value="${user.home}/w4m-conda"/>
-
-	<!--~~~
-	~ ALL ~
-	~~~~~-->
-
-	<target name="all"/>
-
-	<!--~~~~
-	~ TEST ~
-	~~~~~-->
-
-	<target name="test" depends="planemo.lint,planemo.test"/>
-
-	<!--~~~~~~~~~~~~
-	~ PLANEMO LINT ~
-	~~~~~~~~~~~~~-->
-
-	<target name="planemo.lint">
-		<exec executable="planemo" failonerror="true">
-			<arg value="lint"/>
-			<arg value="${tool.xml}"/>
-		</exec>
-	</target>
-
-	<!--~~~~~~~~~~~~
-	~ PLANEMO TEST ~
-	~~~~~~~~~~~~~-->
-
-	<target name="planemo.test" depends="planemo.conda.install">
-		<exec executable="planemo" failonerror="true">
-			<arg value="test"/>
-			<arg value="--conda_prefix"/>
-			<arg value="${conda.dir}"/>
-			<arg value="--galaxy_branch"/>
-			<arg value="release_16.07"/>
-			<arg value="--conda_dependency_resolution"/>
-			<arg value="${tool.xml}"/>
-		</exec>
-	</target>
-
-	<!--~~~~~~~~~~~~~~~~~~~~~
-	~ PLANEMO CONDA INSTALL ~
-	~~~~~~~~~~~~~~~~~~~~~~-->
-
-	<target name="planemo.conda.install" depends="planemo.conda.init">
-		<exec executable="planemo" failonerror="true">
-			<arg value="conda_install"/>
-			<arg value="--conda_prefix"/>
-			<arg value="${conda.dir}"/>
-			<arg value="${tool.xml}"/>
-		</exec>
-	</target>
-
-	<!--~~~~~~~~~~~~~~~~~~
-	~ PLANEMO CONDA INIT ~
-	~~~~~~~~~~~~~~~~~~~-->
-
-	<target name="planemo.conda.init">
-		<exec executable="planemo" failonerror="true">
-			<arg value="conda_init"/>
-			<arg value="--conda_prefix"/>
-			<arg value="${conda.dir}"/>
-		</exec>
-	</target>
-
-	<!--~~~~~~~~~~~~~
-	~ PLANEMO SERVE ~
-	~~~~~~~~~~~~~~-->
-
-	<target name="planemo.serve" depends="planemo.conda.install">
-		<exec executable="planemo" failonerror="true">
-			<arg value="serve"/>
-			<arg value="--conda_prefix"/>
-			<arg value="${conda.dir}"/>
-			<arg value="--galaxy_branch"/>
-			<arg value="release_16.01"/>
-			<arg value="--conda_dependency_resolution"/>
-			<arg value="${tool.xml}"/>
-		</exec>
-	</target>
-
-
-	<!--~~~~~
-	~ CLEAN ~
-	~~~~~~-->
-
-	<target name="clean">
-		<delete dir="${conda.dir}"/>
-	</target>
-
-</project>
Binary file runit/output/figure.pdf has changed
--- a/runit/output/information.txt	Sun Oct 30 14:17:09 2016 -0400
+++ b/runit/output/information.txt	Thu Jan 11 10:21:17 2018 -0500
@@ -1,5 +1,5 @@
 
-Start of the 'Univariate' Galaxy module call: Sun 30 Oct 2016 07:06:06 PM
+Start of the 'Univariate' Galaxy module call: Sat 03 Jun 2017 11:00:34 PM
 
 Performing 'kruskal'
 
@@ -8,4 +8,42 @@
 v5
 v6
 
-End of 'Univariate' Galaxy module call: 2016-10-30 19:06:07
+End of 'Univariate' Galaxy module call: 2017-06-03 23:00:34
+
+
+
+============================================================================
+Additional information about the call:
+
+1) Parameters:
+                     value                          
+dataMatrix_in        "./input/dataMatrix.tsv"       
+sampleMetadata_in    "./input/sampleMetadata.tsv"   
+variableMetadata_in  "./input/variableMetadata.tsv" 
+variableMetadata_out "./output/variableMetadata.tsv"
+figure               "./output/figure.pdf"          
+information          "./output/information.txt"     
+facC                 "qual"                         
+tesC                 "kruskal"                      
+adjC                 "fdr"                          
+thrN                 "0.05"                         
+
+2) Session Info:
+R version 3.3.1 (2016-06-21)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: Ubuntu 16.04.1 LTS
+
+locale:
+ [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
+ [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+ [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
+ [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+ [9] LC_ADDRESS=C               LC_TELEPHONE=C            
+[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
+
+attached base packages:
+[1] stats     graphics  grDevices utils     datasets  base     
+
+other attached packages:
+[1] PMCMR_4.1   batch_1.1-4
+============================================================================
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/.gitignore	Thu Jan 11 10:21:17 2018 -0500
@@ -0,0 +1,1 @@
+*.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/test-univ	Thu Jan 11 10:21:17 2018 -0500
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# Constants {{{1
+################################################################
+
+PROG_PATH=$(dirname $0)
+
+# MAIN {{{1
+################################################################
+
+$PROG_PATH/../univariate_wrapper.R dataMatrix_in $PROG_PATH/../test-data/dataMatrix.tsv sampleMetadata_in $PROG_PATH/../test-data/sampleMetadata.tsv variableMetadata_in $PROG_PATH/../test-data/variableMetadata.tsv facC qual tesC kruskal adjC fdr thrN 0.05 variableMetadata_out $PROG_PATH/outputVariableMetadata.tsv
+
+if ! diff "$PROG_PATH/outputVariableMetadata.tsv" "$PROG_PATH/../test-data/output-variableMetadata.tsv" ; then
+	echo "Incorrect output variable metadata." >&2
+	exit 1
+fi
--- a/univariate_config.xml	Sun Oct 30 14:17:09 2016 -0400
+++ b/univariate_config.xml	Thu Jan 11 10:21:17 2018 -0500
@@ -1,8 +1,7 @@
-<tool id="Univariate" name="Univariate" version="2.2.0">
+<tool id="Univariate" name="Univariate" version="2.2.4">
   <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>
@@ -220,6 +219,14 @@
 NEWS
 ----
 
+CHANGES IN VERSION 2.2.4
+========================
+
+MINOR MODIFICATION
+
+Internal minor modifications for building and testing
+
+
 CHANGES IN VERSION 2.2.0
 ========================
 
@@ -235,7 +242,6 @@
 
 Graphic: a single pdf file containing the graphics of all significant tests is now produced as '_figure.pdf' output: boxplots (respectively scatterplots with the regression line in red and the R2 value) are displayed when the factor of interest is qualitative (respectively quantitative). The corrected p-value is indicated in the title of each plot
 
-
 CHANGES IN VERSION 2.1.4
 ========================
 
@@ -279,19 +285,8 @@
     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">10.1021/acs.jproteome.5b00354</citation>
+    <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
     <citation type="doi">10.1093/bioinformatics/btu813</citation>
   </citations>
   
--- a/univariate_wrapper.R	Sun Oct 30 14:17:09 2016 -0400
+++ b/univariate_wrapper.R	Thu Jan 11 10:21:17 2018 -0500
@@ -2,6 +2,28 @@
 
 library(batch) ## parseCommandArgs
 
+# Constants
+argv <- commandArgs(trailingOnly = FALSE)
+script.path <- sub("--file=","",argv[grep("--file=",argv)])
+prog.name <- basename(script.path)
+
+# Print help
+if (length(grep('-h', argv)) >0) {
+	cat("Usage:", prog.name,
+	    "dataMatrix_in myDataMatrix.tsv",
+	    "sampleMetadata_in mySampleData.tsv",
+	    "variableMetadata_in myVariableMetadata.tsv",
+	    "facC qual",
+	    "tesC kruskal",
+	    "adjC fdr",
+	    "thrN 0.05",
+	    "variableMetadata_out myVariableMetadata_out.tsv",
+	    "figure figure.pdf",
+	    "information information.txt",
+		"\n")
+	quit(status = 0)
+}
+
 source_local <- function(fname){
     argv <- commandArgs(trailingOnly = FALSE)
     base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
@@ -146,6 +168,21 @@
 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
     as.character(Sys.time()), "\n", sep = "")
 
+cat("\n\n\n============================================================================")
+cat("\nAdditional information about the call:\n")
+cat("\n1) Parameters:\n")
+print(cbind(value = argVc))
+
+cat("\n2) Session Info:\n")
+sessioninfo <- sessionInfo()
+cat(sessioninfo$R.version$version.string,"\n")
+cat("Main packages:\n")
+for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+cat("Other loaded packages:\n")
+for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+
+cat("============================================================================\n")
+
 sink()
 
 options(stringsAsFactors = strAsFacL)