Mercurial > repos > ethevenot > biosigner
changeset 3:fa80bd02055f draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 23d58cfd97411ad5d272971896914ce99e30b0ab
| author | ethevenot |
|---|---|
| date | Tue, 06 Jun 2017 11:44:00 -0400 |
| parents | b2414be87d4b |
| children | |
| files | biosigner_config.xml biosigner_wrapper.R build.xml test/.gitignore test/test-biosigner |
| diffstat | 5 files changed, 52 insertions(+), 9 deletions(-) [+] |
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--- a/biosigner_config.xml Sat Aug 06 12:17:12 2016 -0400 +++ b/biosigner_config.xml Tue Jun 06 11:44:00 2017 -0400 @@ -1,8 +1,7 @@ -<tool id="biosigner" name="Biosigner" version="2.2.6"> +<tool id="biosigner" name="Biosigner" version="2.2.7"> <description>Molecular signature discovery from omics data</description> <requirements> - <requirement type="package" version="3.2.2">R</requirement> <requirement type="package">r-batch</requirement> <requirement type="package">bioconductor-biosigner</requirement> </requirements>
--- a/biosigner_wrapper.R Sat Aug 06 12:17:12 2016 -0400 +++ b/biosigner_wrapper.R Tue Jun 06 11:44:00 2017 -0400 @@ -1,4 +1,5 @@ -#!/usr/bin/env Rscript +#!/usr/bin/Rscript --vanilla --slave --no-site-file + library(batch) ## parseCommandArgs @@ -131,13 +132,15 @@ if(!is.null(tierMC)) { plot(bsnLs, tierMaxC = tierMaxC, - file.pdfC = argVc["figure_tier"], + file.pdfC = "figure_tier.pdf", .sinkC = argVc["information"]) + file.rename("figure_tier.pdf", argVc["figure_tier"]) plot(bsnLs, tierMaxC = tierMaxC, typeC = "boxplot", - file.pdfC = argVc["figure_boxplot"], + file.pdfC = "figure_boxplot.pdf", .sinkC = argVc["information"]) + file.rename("figure_boxplot.pdf", argVc["figure_boxplot"]) } else { pdf(argVc["figure_tier"]) plot(1, bty = "n", type = "n", @@ -169,8 +172,7 @@ if(sum(tierMC %in% tierVc)) { cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "") print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), , - drop = FALSE]) - + drop = FALSE]) cat("\nAccuracy:\n") print(round(getAccuracyMN(bsnLs), 3)) } else @@ -216,9 +218,25 @@ 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) rm(list = ls()) -
--- a/build.xml Sat Aug 06 12:17:12 2016 -0400 +++ b/build.xml Tue Jun 06 11:44:00 2017 -0400 @@ -13,7 +13,16 @@ ~ TEST ~ ~~~~~--> - <target name="test" depends="planemo.lint,planemo.test"/> + <target name="test" depends="plain.test,galaxy.test"/> + <target name="galaxy.test" depends="planemo.lint,planemo.test"/> + + <!--~~~~~~~~~~ + ~ PLAIN TEST ~ + ~~~~~~~~~~~--> + + <target name="plain.test"> + <exec executable="test/test-biosigner" failonerror="true"/> + </target> <!--~~~~~~~~~~~~ ~ PLANEMO LINT ~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/.gitignore Tue Jun 06 11:44:00 2017 -0400 @@ -0,0 +1,1 @@ +*.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test-biosigner Tue Jun 06 11:44:00 2017 -0400 @@ -0,0 +1,16 @@ +#!/bin/bash + +# Constants {{{1 +################################################################ + +PROG_PATH=$(dirname $0) + +# MAIN {{{1 +################################################################ + +$PROG_PATH/../biosigner_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 respC gender opcC full methodC all bootI 5 tierC S pvalN 0.05 seedI 123 variableMetadata_out $PROG_PATH/outputVariableMetadata.tsv + +if ! diff "$PROG_PATH/outputVariableMetadata.tsv" "$PROG_PATH/../test-data/variableMetadata.out" ; then + echo "Incorrect output variable metadata." >&2 + exit 1 +fi