| Previous changeset 3:140290de7986 (2016-10-30) Next changeset 5:5687435b182c (2018-02-28) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa |
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modified:
README.md runit/output/figure.pdf runit/output/information.txt univariate_config.xml univariate_wrapper.R |
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added:
Makefile test/.gitignore test/test-univ |
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removed:
build.xml |
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| diff -r 140290de7986 -r 3017385625f6 Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Thu Jan 11 10:21:17 2018 -0500 |
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| @@ -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 + $(RM) -r planemo-venv + +.PHONY: all clean test planemolint planemotest |
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| diff -r 140290de7986 -r 3017385625f6 README.md --- a/README.md Sun Oct 30 14:17:09 2016 -0400 +++ b/README.md Thu Jan 11 10:21:17 2018 -0500 |
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| @@ -7,8 +7,8 @@ ### Description -**Version:** 2.2.0 -**Date:** 2016-10-30 +**Version:** 2.2.4 +**Date:** 2018-01-11 **Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) **Email:** [marie.tremblay-franco(at)toulouse.inra.fr](mailto:marie.tremblay-franco@toulouse.inra.fr); [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) **Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) @@ -50,6 +50,12 @@ ### News +###### CHANGES IN VERSION 2.2.4 + +MINOR MODIFICATION + + * Internal minor modifications for building and testing + ###### CHANGES IN VERSION 2.2.0 MAJOR MODIFICATION |
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| diff -r 140290de7986 -r 3017385625f6 build.xml --- a/build.xml Sun Oct 30 14:17:09 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,95 +0,0 @@ -<project name="w4m.univariate" default="all"> - - <property name="tool.xml" value="univariate_config.xml"/> - <property name="conda.dir" value="${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> |
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| diff -r 140290de7986 -r 3017385625f6 runit/output/figure.pdf |
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| Binary file runit/output/figure.pdf has changed |
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| diff -r 140290de7986 -r 3017385625f6 runit/output/information.txt --- 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 |
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| @@ -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 +============================================================================ |
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| diff -r 140290de7986 -r 3017385625f6 test/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/.gitignore Thu Jan 11 10:21:17 2018 -0500 |
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| @@ -0,0 +1,1 @@ +*.tsv |
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| diff -r 140290de7986 -r 3017385625f6 test/test-univ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test-univ Thu Jan 11 10:21:17 2018 -0500 |
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| @@ -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 |
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| diff -r 140290de7986 -r 3017385625f6 univariate_config.xml --- a/univariate_config.xml Sun Oct 30 14:17:09 2016 -0400 +++ b/univariate_config.xml Thu Jan 11 10:21:17 2018 -0500 |
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| @@ -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> |
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| diff -r 140290de7986 -r 3017385625f6 univariate_wrapper.R --- a/univariate_wrapper.R Sun Oct 30 14:17:09 2016 -0400 +++ b/univariate_wrapper.R Thu Jan 11 10:21:17 2018 -0500 |
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| @@ -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) |