| Next changeset 1:fc66c35dcd4f (2016-07-04) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/nmr_normalization commit 0a2ec9e30fbf7690a80695c751e6ea432b10a759-dirty |
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MANUAL_INSTALL.txt NmrNormalization_script.R NmrNormalization_wrapper.R NmrNormalization_xml.xml README.rst planemo_test.sh test-data/MTBLS1_bucketedData.tabular test-data/MTBLS1_bucketedData_normalized.tabular test-data/MTBLS1_sampleMetadata_normalized.tabular test-data/MTBLS1_variableMetadata_normalized.tabular tool_dependencies.xml |
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| diff -r 000000000000 -r e1b29d705286 MANUAL_INSTALL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MANUAL_INSTALL.txt Mon Apr 18 11:29:30 2016 -0400 |
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| @@ -0,0 +1,44 @@ +Instructions to integrate the NMR Normalization" tool into a local instance of Galaxy +Version mars 2015 M Tremblay-Franco + + +## --- R bin and Packages : --- ## +R version 3.0.2 (2013-09-25) -- "Frisbee Sailing +Platform: x86_64-redhat-linux-gnu (64-bit) + +Install the "batch" library, necessary for parseCommandArgs function: + - Download package source (*.tar.gz file) from your favorite CRAN (http://www.r-project.org/) +For example: http://cran.univ-lyon1.fr/ + + - Install package in your R session +install.packages("path/package_name.tar.gz",lib="path",repos=NULL) +For Example: install.packages("/usr/lib64/R/library/batch_1.1-4.tar",lib="/usr/lib64/R/library",repos=NULL) + + - Finally, load the package into your R session +library(batch) + + + +## --- Config : --- ## + - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add +<section id="id_name" name="Name"> + <tool file="path/NmrNormalization_xml.xml" /> +</section> +to create a new section containing the Nmr_Normalization tool +or add + <tool file="path/NmrNormalization_xml.xml" /> +in an existing section + + - Put the three files NmrNormalization_xml.xml, NmrNormalization_wrapper.R and NmrNormalization_script.R in a same directory +For example, path=/galaxy/dist/galaxy-dist/tools/stats + + - Edit the NmrBucketing_xml.xml file and change the path in the following lines + # R script + R --vanilla --slave --no-site-file --file=path/NmrNormalization_wrapper.R --args + + ## Library name for raw files storage + library path/$library + + + +Finally, restart Galaxy \ No newline at end of file |
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| diff -r 000000000000 -r e1b29d705286 NmrNormalization_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrNormalization_script.R Mon Apr 18 11:29:30 2016 -0400 |
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| b'@@ -0,0 +1,185 @@\n+#################################################################################################################\r\n+# SPECTRA NORMALIZATION FROM BUCKETED AND INTEGRATED SPECTRA #\r\n+# User : Galaxy #\r\n+# Original data : -- #\r\n+# Starting date : 20-10-2014 #\r\n+# Version 1 : 27-01-2015 #\r\n+# Version 2 : 27-02-2015 #\r\n+# #\r\n+# Input files: #\r\n+# - Data matrix containing bucketed and integrated spectra to normalize #\r\n+# - Sample metadata matrix containing at least biological factor of interest #\r\n+# - Scaling method: Total intensity/Probabilistic Quotient Normalization #\r\n+# - Control group: name of control to compute median reference spectra #\r\n+# - Graph: normalization result representation #\r\n+#################################################################################################################\r\n+NmrNormalization <- function(dataMatrix,scalingMethod=c("None","Total","PQN","BioFactor"),sampleMetadata=NULL,\r\n+ bioFactor=NULL,ControlGroup=NULL,graph=c("None","Overlay","One_per_individual"),\r\n+ nomFichier=NULL,savLog.txtC=NULL)\r\n+{\r\n+\r\n+ ## Option\r\n+ ##---------------\r\n+ strAsFacL <- options()$stringsAsFactors\r\n+ options(stingsAsFactors = FALSE)\r\n+ options(warn = -1)\r\n+ \r\n+ \r\n+ ## Constants\r\n+ ##---------------\r\n+ topEnvC <- environment()\r\n+ flgC <- "\\n"\r\n+ \r\n+ ## Log file (in case of integration into Galaxy)\r\n+ ##----------------------------------------------\r\n+ if(!is.null(savLog.txtC))\r\n+ sink(savLog.txtC, append = TRUE)\r\n+ \r\n+ ## Functions definition\r\n+ ##--------------------- \r\n+ #################################################################################################################\r\n+ # Total intensity normalization\r\n+ # Input parameters\r\n+ # - data : bucketed spectra (rows=buckets; columns=samples)\r\n+ ################################################################################################################# \r\n+ NmrBrucker_total <- function(data)\r\n+ {\r\n+ # Total intensity normalization\r\n+ data.total <- apply(data,2,sum)\r\n+ data.normalized <- data[,1]/data.total[1]\r\n+ for (i in 2:ncol(data))\r\n+ data.normalized <- cbind(data.normalized,data[,i]/data.total[i]) \r\n+ colnames(data.normalized) <- colnames(data)\r\n+ rownames(data.normalized) <- rownames(data)\r\n+ return(data.normalized)\r\n+ }\r\n+\r\n+ \r\n+ #################################################################################################################\r\n+ # Biological factor normalization\r\n+ # Input parameters\r\n+ # - data : bucketed spectra (rows=buckets; columns=samples)\r\n+ # - sampleMetadata : dataframe with biological factor of interest measured for each invidual\r\n+ # - bioFactor : name of the column cotaining the biological factor of interest\r\n+ #################################################################################################################\r\n+ NmrBrucker_bioFact <- function(data,sampleMetadata,bioFactor)\r\n+ {\r\n+ # Total intensity normalization\r\n+ data.normalized <- data['..b'###############################################################################\r\n+ # Probabilistic quotient normalization (PQN)\r\n+ # Input parameters\r\n+ # - data : bucketed spectra (rows=buckets; columns=samples)\r\n+ # - sampleMetadata : dataframe with treatment group of inviduals\r\n+ # - pqnFactor : number of the column cotaining the biological facor of interest\r\n+ # - nomControl : name of the treatment group\r\n+ #################################################################################################################\r\n+ NmrBrucker_pqn <- function(data,sampleMetadata,pqnFactor,nomControl)\r\n+ {\r\n+ # Total intensity normalization\r\n+ data.total <- apply(data,2,sum)\r\n+ data.normalized <- data[,1]/data.total[1]\r\n+ for (i in 2:ncol(data))\r\n+ data.normalized <- cbind(data.normalized,data[,i]/data.total[i]) \r\n+ colnames(data.normalized) <- colnames(data)\r\n+ rownames(data.normalized) <- rownames(data)\r\n+ \r\n+ # Reference spectrum\r\n+ # Recuperation spectres individus controle\r\n+ control.spectra <- data.normalized[,sampleMetadata[,pqnFactor]==nomControl]\r\n+ spectrum.ref <- apply(control.spectra,1,median)\r\n+ \r\n+ # Ratio between normalized and reference spectra\r\n+ data.normalized.ref <- data.normalized/spectrum.ref\r\n+ \r\n+ # Median ratio\r\n+ data.normalized.ref.median <- apply(data.normalized.ref,1,median)\r\n+ \r\n+ # Normalization\r\n+ data.normalizedPQN <- data.normalized[,1]/data.normalized.ref.median\r\n+ for (i in 2:ncol(data))\r\n+ data.normalizedPQN <- cbind(data.normalizedPQN,data.normalized[,i]/data.normalized.ref.median)\r\n+ colnames(data.normalizedPQN) <- colnames(data)\r\n+ rownames(data.normalizedPQN) <- rownames(data)\r\n+ \r\n+ return(data.normalizedPQN)\r\n+ }\r\n+ \r\n+ \r\n+ ## Tests\r\n+ if (scalingMethod=="QuantitativeVariable")\r\n+ {\r\n+ if(mode(sampleMetadata[,bioFactor]) == "character")\r\n+ bioFact <- factor(sampleMetadata[,bioFactor])\r\n+ else\r\n+ bioFact <- sampleMetadata[,bioFactor]\r\n+ }\r\n+ \r\n+ ## Spectra scaling depending on the user choice\r\n+ if (scalingMethod == "None")\r\n+ {\r\n+ NormalizedBucketedSpectra <- dataMatrix\r\n+ }\r\n+ else if (scalingMethod == "Total")\r\n+ {\r\n+ NormalizedBucketedSpectra <- NmrBrucker_total(dataMatrix) \r\n+ }\r\n+ else if (scalingMethod == "PQN")\r\n+ {\r\n+ NormalizedBucketedSpectra <- NmrBrucker_pqn(dataMatrix,sampleMetadata,bioFactor,ControlGroup)\r\n+ }\r\n+ else if (scalingMethod == "QuantitativeVariable")\r\n+ {\r\n+ NormalizedBucketedSpectra <- NmrBrucker_bioFact(dataMatrix,sampleMetadata,bioFact)\r\n+ }\r\n+ \r\n+ # Graphic\r\n+ if (graph != "None")\r\n+ {\r\n+ # Graphic Device opening\r\n+ pdf(nomFichier,onefile=TRUE)\r\n+ if (graph == "Overlay")\r\n+ {\r\n+ ymax <- max(NormalizedBucketedSpectra)\r\n+ plot(1:length(NormalizedBucketedSpectra[,1]),NormalizedBucketedSpectra[,1],ylim=c(0,ymax),\r\n+ type=\'l\',col=1,xlab="Chemical shift",ylab="Intensity")\r\n+ for (i in 2:ncol(NormalizedBucketedSpectra))\r\n+ {\r\n+ spectre <- NormalizedBucketedSpectra[,i]\r\n+ lines(spectre,col=i)\r\n+ }\r\n+ }\r\n+ else\r\n+ {\r\n+ for (i in 1:ncol(NormalizedBucketedSpectra))\r\n+ {\r\n+ plot(1:length(NormalizedBucketedSpectra[,i]),NormalizedBucketedSpectra[,i],type=\'l\',col=1,\r\n+ xlab="Chemical shift",ylab="Intensity")\r\n+ }\r\n+ }\r\n+ dev.off()\r\n+ }\r\n+ \r\n+ # Output datasets creation\r\n+ if (scalingMethod == "None" || scalingMethod == "Total")\r\n+ {\r\n+ sampleMetadata <- data.frame(1:ncol(NormalizedBucketedSpectra))\r\n+ rownames(sampleMetadata) <- colnames(NormalizedBucketedSpectra)\r\n+ colnames(sampleMetadata) <- "SampleOrder"\r\n+ }\r\n+ \r\n+ variableMetadata <- data.frame(1:nrow(NormalizedBucketedSpectra))\r\n+ rownames(variableMetadata) <- rownames(NormalizedBucketedSpectra)\r\n+ colnames(variableMetadata) <- "VariableOrder"\r\n+\r\n+ return(list(NormalizedBucketedSpectra,sampleMetadata,variableMetadata))\r\n+\r\n+}\r\n' |
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| diff -r 000000000000 -r e1b29d705286 NmrNormalization_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrNormalization_wrapper.R Mon Apr 18 11:29:30 2016 -0400 |
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| @@ -0,0 +1,128 @@ +#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file + +## 070115_NmrBucketing2galaxy_v1.R +## Marie Tremblay-Franco +## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics +## www.metabohub.fr/en +## marie.tremblay-franco@toulouse.inra.fr + +runExampleL <- FALSE + + +##------------------------------ +## Options +##------------------------------ +strAsFacL <- options()$stringsAsFactors +options(stringsAsFactors = FALSE) + + +##------------------------------ +## Libraries laoding +##------------------------------ +# For parseCommandArgs function +library(batch) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} +#Import the different functions +source_local("NmrNormalization_script.R") + +##------------------------------ +## Errors ????????????????????? +##------------------------------ + + +##------------------------------ +## Constants +##------------------------------ +topEnvC <- environment() +flagC <- "\n" + + +##------------------------------ +## Script +##------------------------------ +if(!runExampleL) + argLs <- parseCommandArgs(evaluate=FALSE) + + +## Parameters Loading +##------------------- + # Inputs +data <- read.table(argLs[["dataMatrix"]],check.names=FALSE,header=TRUE,sep="\t") +rownames(data) <- data[,1] +data <- data[,-1] + +scaling <- argLs[["scalingMethod"]] +graphique <- argLs[["graphType"]] + +if (scaling=='PQN') +{ + metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t") + factor<- argLs[["factor"]] + ControlGroup <- argLs[["controlGroup"]] +} +if (scaling=='QuantitativeVariable') +{ + metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t") + factor <- argLs[["factor"]] +} + + # Outputs +nomGraphe <- argLs[["graphOut"]] +dataMatrixOut <- argLs[["dataMatrixOut"]] +sampleMetadataOut <- argLs[["sampleMetadataOut"]] +variableMetadataOut <- argLs[["variableMetadataOut"]] +log <- argLs[["logOut"]] + +## Checking arguments +##------------------- +error.stock <- "\n" + +if(length(error.stock) > 1) + stop(error.stock) + + +## Computation +##------------ +NormalizationResults <- NmrNormalization(dataMatrix=data,scalingMethod=scaling,sampleMetadata=metadataSample, + bioFactor=factor,ControlGroup=ControlGroup, + graph=graphique,nomFichier=nomGraphe,savLog.txtC=log) + +data_normalized <- NormalizationResults[[1]] +data_sample <- NormalizationResults[[2]] +data_variable <- NormalizationResults[[3]] + + + +## Saving +##------- + # Data +data_normalized <- cbind(rownames(data_normalized),data_normalized) +colnames(data_normalized) <- c("Bucket",colnames(data_normalized)[-1]) +write.table(data_normalized,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t") + # Sample +data_sample <- cbind(rownames(data_sample),data_sample) +colnames(data_sample) <- c("Sample",colnames(data_sample)[-1]) +write.table(data_sample,file=argLs$sampleMetadataOut,quote=FALSE,row.names=FALSE,sep="\t") + # Variable +data_variable <- cbind(rownames(data_variable),data_variable) +colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1]) +write.table(data_variable,file=argLs$variableMetadataOut,quote=FALSE,row.names=FALSE,sep="\t") + + +## Ending +##--------------------- + +cat("\nEnd of 'NMR Normalization' Galaxy module call: ", as.character(Sys.time()), sep = "") + +## sink(NULL) + +options(stringsAsFactors = strAsFacL) + +rm(list = ls()) |
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| diff -r 000000000000 -r e1b29d705286 NmrNormalization_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NmrNormalization_xml.xml Mon Apr 18 11:29:30 2016 -0400 |
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| b'@@ -0,0 +1,263 @@\n+<tool id="NmrNormalization" name="NMR_Normalization" version="1.0.1">\n+ \n+ <description>Normalization of NMR bucketed and integrated spectra</description>\n+\n+ <requirements>\r\n+ <requirement type="package" version="3.1.2">R</requirement>\r\n+\t <requirement type="package" version="1.1_4">r-batch</requirement>\r\n+ </requirements>\n+ \n+\t <stdio>\r\n+ <exit_code range="1:" level="fatal" />\r\n+ </stdio>\r\n+\r\n+ <command>\r\n+ Rscript $__tool_directory__/NmrNormalization_wrapper.R\n+\n+\t\t ## Data matrix of bucketed and integrated spectra\n+\t\t dataMatrix $dataMatrix\n+\n+\t\t ## Normalization method\n+\t\t scalingMethod $scalingMethod.method\n+\t\t #if $scalingMethod.method == "PQN":\n+\t\t\t ## Sample metadata matrix\n+\t\t\t sampleMetadata $scalingMethod.sampleMetadata\n+\n+\t\t\t ## Biological factor of interest (column number in samplemetadata)\n+\t\t\t factor $scalingMethod.factor\n+\n+\t\t\t ## Reference class\n+\t\t\t controlGroup $scalingMethod.controlGroup\n+\t\t #end if\n+\t\t #if $scalingMethod.method == "QuantitativeVariable":\n+\t\t\t ## Sample metadata matrix\n+\t\t\t sampleMetadata $scalingMethod.sampleMetadata\n+\n+\t\t\t ## Biological factor of interest (column number in samplemetadata)\n+\t\t\t factor $scalingMethod.factor \n+\t\t #end if\n+\t\t\n+\t\t ## Spectra representation\n+\t\t graphType $graphType\n+\n+\t\t ## Outputs\n+\t\t logOut $logOut\n+\t\t dataMatrixOut $dataMatrixOut\n+\t\t sampleMetadataOut $sampleMetadataOut\n+\t\t variableMetadataOut $variableMetadataOut\n+\t\t graphOut $graphOut\n+\n+\n+\t</command>\n+ \n+\t<inputs>\n+\t\t<param name="dataMatrix" type="data" label="Data matrix of bucketed and integrated spectra" help="" format="tabular" />\n+\n+\n+\t\t<conditional name="scalingMethod" >\n+\t\t\t<param name="method" label="Normalization method" type="select" help="Default method is total intensity" >\n+\t\t\t\t<option value="None" lable="None normalization"/>\n+\t\t\t\t<option value="Total" label="Total intensity"/>\n+\t\t\t\t<option value="PQN" label="Probabilistic Quotient Normalization "/>\n+\t\t\t\t<option value="QuantitativeVariable" label="Quantitative variable" />\n+\t\t\t</param>\n+ <when value="None" />\n+ <when value="Total" />\n+\t\t\t<when value="PQN">\n+\t\t\t\t<param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />\n+\t\t\t\t<param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" />\n+\t\t\t\t<param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/>\n+\t\t\t</when>\n+\t\t\t<when value="QuantitativeVariable">\n+\t\t\t\t<param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />\n+\t\t\t\t<param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" />\n+\t\t\t</when>\n+\t\t</conditional>\n+\n+\t\t<param name="graphType" label="Spectra representation" type="select" help="Select \'None\' for no representation,\'Overlay\' to overlay all spectra on a unique chart and \'One per individual\' to generate an individual chart for each observation">\n+\t\t\t<option value="None"> none </option>\n+\t\t\t<option value="Overlay"> Overlay </option>\n+\t\t\t<option value="One_per_individual"> One_per_individual </option>\n+\t\t</param>\n+\t</inputs>\n+ \n+ \n+\t<outputs>\n+\t\t<data format="txt" name="logOut" label="${tool.name}_log" />\n+\t\t<data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />\n+\t\t<data format="tabular" name="sampleMetadataOut" label="${tool.name}_samplemetadata" />\n+\t\t<data format="tabular" name="variableMetadataOut" label="${tool.name}_variableMetadataOut" />\n+\t\t<data format="pdf" name="graphOut" label="${tool.name}_spectra" >\n+\t\t\t<filter> graphType != "None" </filter>\n+\t\t</data>\n+\t</outputs>\n+ \n+ <tests>\r\n+ <test>\r\n+ <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" />\r\n+ <param name="scalingMethod|method" valu'..b'==+=============+\n+| NMR_Bucketing | NMR_Normalization_bucketedData.tsv | tabular | Ions Matrix |\n++----------------------+------------------------------------+---------+-------------+\n+\n+\n+\n+\n+**Downstream tools**\n+\n++---------------------------+----------------------+--------+\n+| Name | Output file | Format |\n++===========================+======================+========+\n+|Univariate | variableMetadata.tsv | Tabular|\n++---------------------------+----------------------+--------+\n+|Multivariate | sampleMetadata.tsv | Tabular|\n++---------------------------+----------------------+--------+\n+| | variableMetadata.tsv | Tabular|\n++---------------------------+----------------------+--------+\n+\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+------------+\n+| Parameter : num + label | Format |\n++===========================+============+\n+| DataMatrix | Tabular |\n++---------------------------+------------+\n+\n+**DataMAtrix**\n+\n+\t| variable x sample dataMatrix tabular separated file containing bucketed and integrated NMR spectra, with . as decimal, and NA for missing values\n+\n+\n+----------\n+Parameters\n+----------\n+\n+DataMatrix\n+\t| see "Input files" section above\n+\t| \n+\n+Normalization method\n+\t| normalization to apply on each spectrum: \n+\n++---------------------------+--------------------------------------+\n+| Name | Normalization |\n++===========================+======================================+\n+|None | No |\n++---------------------------+--------------------------------------+\n+|Total | Total intensity |\n++---------------------------+--------------------------------------+\n+|PQN | Probabilistic Quotient Normalization |\n++---------------------------+--------------------------------------+\n+|QuantitativeVariable | Weight, osmolality, ... |\n++---------------------------+--------------------------------------+\n+\n+\n+sampleMetadata\n+\t| sample x metadata **sample** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values\n+\t| Mandatory for "PQN" or "Quantitative" normalization method\n+\t| The row names must be identical to the column names of the dataMatrix file\n+\t|\n+\n+\n+Spectra representation:\n+\t| Graphical chart of bucketed and integrated raw files\n+\t| If "Overlay": the n (sample number) spectra are overlaid on the same figure\n+\t| If "One_per_individual": pdf file includes n pages (1 per sample)\n+\t|\n+\n+\n+------------\n+Output files\n+------------\n+\n+\n+bucketedData.tsv\n+\t| tabular output\n+\t| Data matrix with p rows (buckets) and n columns (samples) containing the intensities\n+\t|\n+\n+sampleMetadata.tsv\n+\t| tabular output\n+\t| sampleMetadata file identical to the file given as argument if "PQN" or "Quantitative" normalization method; file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order if "None" or "Total" normalization methof\n+\t| Mandatory file in the statistical analysis step of the workflow\n+\t|\n+\n+variableMetadata.tsv\n+\t| tabular output\n+\t| file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order. Can add columns with numeric and/or character variable metadata. \n+\t| Mandatory file in the statistical analysis step of the workflow\n+\t|\n+\n+spectra.pdf\n+\t| pdf output\n+\t| Graphical chart of bucketed and integrated data\n+\t| \n+\n+\n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+\n+.. class:: warningmark\n+\n+Under construction\n+\n+.. image:: ./static/images/Mth_Travaux.png\n+ :width: 100\n+\n+\n+ </help>\r\n+ <citations>\r\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\r\n+ </citations>\n+</tool>\n+\n' |
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| diff -r 000000000000 -r e1b29d705286 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Apr 18 11:29:30 2016 -0400 |
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| @@ -0,0 +1,20 @@ + +Changelog/News +-------------- + +**Version 1.0.1 - 14/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + +**Version 2015-01-28 - 28/01/2015** + + + +Test Status +----------- + +Planemo test using conda: passed + +Planemo shed_test: passed + |
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| diff -r 000000000000 -r e1b29d705286 planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Mon Apr 18 11:29:30 2016 -0400 |
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| @@ -0,0 +1,12 @@ +planemo conda_init +planemo conda_install . +planemo test --install_galaxy --conda_dependency_resolution + +#All 1 test(s) executed passed. +#NmrNormalization[0]: passed + +planemo shed_test --install_galaxy -t testtoolshed + +#All 1 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/nmr_normalization/NmrNormalization/1.0.1[0]: passed + |
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| diff -r 000000000000 -r e1b29d705286 test-data/MTBLS1_bucketedData.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_bucketedData.tabular Mon Apr 18 11:29:30 2016 -0400 |
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| b'@@ -0,0 +1,595 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|
| b |
| diff -r 000000000000 -r e1b29d705286 test-data/MTBLS1_bucketedData_normalized.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_bucketedData_normalized.tabular Mon Apr 18 11:29:30 2016 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r e1b29d705286 test-data/MTBLS1_sampleMetadata_normalized.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_sampleMetadata_normalized.tabular Mon Apr 18 11:29:30 2016 -0400 |
| b |
| @@ -0,0 +1,24 @@ +Sample SampleOrder +ADG10003u_007 1 +ADG10003u_008 2 +ADG10003u_009 3 +ADG10003u_010 4 +ADG10003u_015 5 +ADG10003u_016 6 +ADG10003u_017 7 +ADG10003u_021 8 +ADG10003u_022 9 +ADG10003u_023 10 +ADG10003u_051 11 +ADG10003u_052 12 +ADG10003u_053 13 +ADG10003u_066 14 +ADG10003u_067 15 +ADG10003u_071 16 +ADG10003u_072 17 +ADG10003u_073 18 +ADG10003u_087 19 +ADG10003u_088 20 +ADG10003u_089 21 +ADG10003u_097 22 +ADG10003u_098 23 |
| b |
| diff -r 000000000000 -r e1b29d705286 test-data/MTBLS1_variableMetadata_normalized.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS1_variableMetadata_normalized.tabular Mon Apr 18 11:29:30 2016 -0400 |
| b |
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| b |
| diff -r 000000000000 -r e1b29d705286 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Apr 18 11:29:30 2016 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="r-batch" version="1.1_4"> + <repository changeset_revision="e8a964ca8656" name="package_r_batch_1_1_4" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |