# HG changeset patch
# User ethevenot
# Date 1508849042 14400
# Node ID 059eb452931ef50ec10441765b9791dcf3c18fcc
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
diff -r 000000000000 -r 059eb452931e LICENSE.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE.md Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,517 @@
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+Version 2.1 dated 2013-06-21
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+ Notice
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+This Agreement is a Free Software license agreement that is the result
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+ 11.1 EXCUSABLE EVENTS
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+
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+
+
+ 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
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+
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+
+12.3 Any Software distributed under a given version of the Agreement may
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+or a subsequent version, subject to the provisions of Article 5.3.4
+<#compatibility>.
+
+
+ Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
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+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
diff -r 000000000000 -r 059eb452931e README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Tue Oct 24 08:44:02 2017 -0400
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+Checking the formats of the dataMatrix, sampleMetadata, and variableMetadata files
+==================================================================================
+
+A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
+
+Status: [](https://travis-ci.org/workflow4metabolomics/checkformat).
+
+### Description
+
+**Version:** 2.0.4
+**Date:** 2016-07-29
+**Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
+**Email:** [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)
+**Licence:** CeCILL
+**Reference histories:**
+[W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published),
+[W4M00002_sacurine_mtbls2](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00003_sacurine_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published)
+**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
+
+* Configuration file: `checkformat_config.xml`
+* Image file: `static/images/checkformat_workflowPositionImage.png`
+* Wrapper file: `checkformat_wrapper.R`
+* R packages
+ + **batch** from CRAN
+
+ ```r
+ install.packages("batch", dep=TRUE)
+ ```
+
+### Tests
+
+The code in the wrapper can be tested by running the `runit/checkformat_tests.R` R file
+
+You will need to install **RUnit** package in order to make it run:
+```r
+install.packages('RUnit', dependencies = TRUE)
+```
+
+### Working example
+
+See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2**, or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
+
+### News
+
+##### CHANGES IN VERSION 2.0.4
+
+INTERNAL MODIFICATION
+
+ * Minor internal modifications
+
+##### CHANGES IN VERSION 2.0.2
+
+INTERNAL MODIFICATION
+
+ * Creating tests for R code
\ No newline at end of file
diff -r 000000000000 -r 059eb452931e build.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/build.xml Tue Oct 24 08:44:02 2017 -0400
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diff -r 000000000000 -r 059eb452931e checkformat_config.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/checkformat_config.xml Tue Oct 24 08:44:02 2017 -0400
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+
+ Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files
+
+
+ r-batch
+
+
+
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+
+
+
+.. class:: infomark
+
+**Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**Tool updates**
+
+See the **NEWS** section at the bottom of this page
+
+---------------------------------------------------
+
+========================
+Check Format
+========================
+
+-----------
+Description
+-----------
+
+| Checks the format (row and column names) of the dataMatrix, sampleMetadata and variableMetadata tables
+
+
+-----------------
+Workflow position
+-----------------
+
+.. image:: ./static/images/checkFormat_workflowPositionImage.png
+:width: 600
+
+
+
+-----------
+Input files
+-----------
+
++----------------------------+---------+
+| Parameter : num + label | Format |
++============================+=========+
+| 1 : Data matrix file | tabular |
++----------------------------+---------+
+| 2 : Sample metadata file | tabular |
++----------------------------+---------+
+| 3 : Variable metadata file | tabular |
++----------------------------+---------+
+
+|
+| **Required formats for the dataMatrix, sampleMetadata, and variableMetadata files are**
+| **described in the HowTo entitled 'Format Data For Postprocessing' available on the**
+| **main page of Workflow4Metabolomics.org**
+|
+
+------------
+Output files
+------------
+
+information.txt
+| Text file with all messages when error(s) in formats are detected
+|
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+.. class:: infomark
+
+See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2**, or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
+
+---------------------------------------------------
+
+----
+NEWS
+----
+
+CHANGES IN VERSION 2.0.4
+========================
+
+INTERNAL MODIFICATIONS
+
+Minor internal modifications
+
+CHANGES IN VERSION 2.0.2
+========================
+
+INTERNAL MODIFICATIONS
+
+Test for R code
+Planemo running validation
+Planemo installing validation
+Travis automated testing
+Toolshed export
+
+
+
+
+ @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 = {Thévenot, Etienne A. and Roux, Aurélie 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}
+ }
+ 10.1093/bioinformatics/btu813
+
+
+
+
diff -r 000000000000 -r 059eb452931e checkformat_script.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/checkformat_script.R Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,186 @@
+## Etienne Thevenot
+## CEA, MetaboHUB Paris
+## etienne.thevenot@cea.fr
+
+
+## Reads the dataMatrix, sampleMetadata, and variableMetadata .tsv files
+## and checks the formats
+readAndCheckF <- function(datFilC="dataMatrix.tsv",
+ samFilC="sampleMetadata.tsv",
+ varFilC="variableMetadata.tsv") {
+
+ ## options
+
+ optStrAsFacL <- options()[["stringsAsFactors"]]
+ options(stringsAsFactors = FALSE)
+
+ ## checking that the tables have no duplicated row or column names
+
+ for(tabC in c("dat", "sam", "var")) {
+
+ tabNamC <- switch(tabC, dat="dataMatrix", sam="sampleMetadata", var="variableMetadata")
+
+ rowVc <- read.table(eval(parse(text=paste0(tabC, "FilC"))),
+ check.names = FALSE,
+ header = TRUE,
+ sep = "\t")[, 1]
+
+ colVc <- unlist(read.table(eval(parse(text=paste0(tabC, "FilC"))),
+ check.names = FALSE,
+ nrow=1,
+ sep = "\t"))[-1]
+
+ if(any(duplicated(rowVc)))
+ stop("The following row name(s) is/are duplicated in the ",
+ tabNamC,
+ " table: '",
+ paste(rowVc[duplicated(rowVc)], collapse="', '"), "'",
+ call.=FALSE)
+
+ if(any(duplicated(colVc)))
+ stop("The following column name(s) is/are duplicated in the ",
+ tabNamC,
+ " table: '",
+ paste(colVc[duplicated(colVc)], collapse="', '"), "'",
+ call.=FALSE)
+
+ rowMakVc <- make.names(rowVc, unique = TRUE)
+
+ rowDifVl <- rowVc != rowMakVc
+
+ if(any(rowDifVl)) {
+ rowDifDF <- data.frame(row = 1:length(rowVc),
+ actual = rowVc,
+ preferred = rowMakVc)
+ rowDifDF <- rowDifDF[rowDifVl, , drop = FALSE]
+ cat("\n\nWarning: The following row names of the ",
+ tabNamC,
+ " table are not in the standard R format, which may result in errors when loading the data in some of the W4M modules:\n", sep="")
+ print(rowDifDF)
+ }
+
+ colMakVc <- make.names(colVc, unique = TRUE)
+
+ colDifVl <- colVc != colMakVc
+
+ if(any(colDifVl)) {
+ colDifDF <- data.frame(col = 1:length(colVc),
+ actual = colVc,
+ preferred = colMakVc)
+ colDifDF <- colDifDF[colDifVl, , drop = FALSE]
+ cat("\n\nWarning: The following column names of the ",
+ tabNamC,
+ " table are not in the standard R format, which may result in errors when loading the data in some of the W4M modules:\n", sep="")
+ print(colDifDF)
+ }
+ }
+
+ ## reading tables
+
+ datMN <- t(as.matrix(read.table(datFilC,
+ check.names = FALSE,
+ header = TRUE,
+ row.names = 1,
+ sep = "\t")))
+
+ samDF <- read.table(samFilC,
+ check.names = FALSE,
+ header = TRUE,
+ row.names = 1,
+ sep = "\t")
+
+ varDF <- read.table(varFilC,
+ check.names = FALSE,
+ header = TRUE,
+ row.names = 1,
+ sep = "\t")
+
+ ## checking formats
+
+ chkL <- TRUE
+
+ if(!identical(rownames(datMN), rownames(samDF))) {
+ ## checking sample names
+
+ chkL <- FALSE
+
+ datSamDifVc <- setdiff(rownames(datMN), rownames(samDF))
+
+ if(length(datSamDifVc)) {
+ cat("\nThe following samples were found in the dataMatrix column names but not in the sampleMetadata row names:\n", sep="")
+ print(cbind.data.frame(col = as.numeric(sapply(datSamDifVc, function(samC) which(rownames(datMN) == samC))),
+ name = datSamDifVc))
+ }
+
+ samDatDifVc <- setdiff(rownames(samDF), rownames(datMN))
+
+ if(length(samDatDifVc)) {
+ cat("\n\nThe following samples were found in the sampleMetadata row names but not in the dataMatrix column names:\n", sep="")
+ print(cbind.data.frame(row = as.numeric(sapply(samDatDifVc, function(samC) which(rownames(samDF) == samC))),
+ name = samDatDifVc))
+ }
+
+ if(nrow(datMN) != nrow(samDF)) {
+ cat("\n\nThe dataMatrix has ", nrow(datMN), " columns (ie samples) whereas the sampleMetadata has ", nrow(samDF), " rows\n", sep="")
+ } else if(identical(gsub("^X", "", rownames(datMN)), rownames(samDF))) {
+ cat("\n\nThe dataMatrix column names start with an 'X' but not the sampleMetadata row names\n", sep="")
+ } else if(identical(gsub("^X", "", rownames(samDF)), rownames(datMN))) {
+ cat("\n\nThe sampleMetadata row names start with an 'X' but not the dataMatrix column names\n", sep="")
+ } else if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) {
+ cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not in the same order:\n", sep="")
+ print(cbind.data.frame(indice = 1:nrow(datMN),
+ dataMatrix_columnnames=rownames(datMN),
+ sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
+ } else {
+ cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not identical:\n", sep="")
+ print(cbind.data.frame(indice = 1:nrow(datMN),
+ dataMatrix_columnnames=rownames(datMN),
+ sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE])
+ }
+
+ }
+
+ if(!identical(colnames(datMN), rownames(varDF))) {
+ ## checking variable names
+
+ chkL <- FALSE
+
+ datVarDifVc <- setdiff(colnames(datMN), rownames(varDF))
+
+ if(length(datVarDifVc)) {
+ cat("\nThe following variables were found in the dataMatrix row names but not in the variableMetadata row names:\n", sep="")
+ print(cbind.data.frame(row = as.numeric(sapply(datVarDifVc, function(varC) which(colnames(datMN) == varC))),
+ name = datVarDifVc))
+
+ }
+
+ varDatDifVc <- setdiff(rownames(varDF), colnames(datMN))
+
+ if(length(varDatDifVc)) {
+ cat("\n\nThe following variables were found in the variableMetadata row names but not in the dataMatrix row names:\n", sep="")
+ print(cbind.data.frame(row = as.numeric(sapply(varDatDifVc, function(varC) which(rownames(varDF) == varC))),
+ name = varDatDifVc))
+ }
+
+ if(ncol(datMN) != nrow(varDF)) {
+ cat("\n\nThe dataMatrix has ", nrow(datMN), " rows (ie variables) whereas the variableMetadata has ", nrow(varDF), " rows\n", sep="")
+ } else if(identical(sort(colnames(datMN)), sort(rownames(varDF)))) {
+ cat("\n\nThe dataMatrix row names and the variableMetadata row names are not in the same order:\n", sep="")
+ print(cbind.data.frame(row = 1:ncol(datMN),
+ dataMatrix_rownames=colnames(datMN),
+ variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE])
+ } else {
+ cat("\n\nThe dataMatrix row names and the variableMetadata row names are not identical:\n", sep="")
+ print(cbind.data.frame(row = 1:ncol(datMN),
+ dataMatrix_rownames=colnames(datMN),
+ variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE])
+ }
+ }
+
+ options(stringsAsFactors=optStrAsFacL)
+
+ resLs <- list(chkL=chkL)
+
+ return(resLs)
+
+} ## end of checkAndReadF
diff -r 000000000000 -r 059eb452931e checkformat_wrapper.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/checkformat_wrapper.R Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,107 @@
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+source_local <- function(fname){
+ argv <- commandArgs(trailingOnly = FALSE)
+ base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+ source(paste(base_dir, fname, sep="/"))
+}
+
+source_local("checkformat_script.R")
+
+argVc <- unlist(parseCommandArgs(evaluate = FALSE))
+
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## options
+##--------
+
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+## constants
+##----------
+
+modNamC <- "Check Format" ## module name
+
+## log file
+##---------
+
+sink(argVc["information"])
+
+cat("\nStart of the '", modNamC, "' Galaxy module call: ",
+ format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+
+##------------------------------
+## Computation
+##------------------------------
+
+
+resLs <- readAndCheckF(argVc["dataMatrix_in"],
+ argVc["sampleMetadata_in"],
+ argVc["variableMetadata_in"])
+chkL <- resLs[["chkL"]]
+
+
+##------------------------------
+## Ending
+##------------------------------
+
+
+if(chkL) {
+
+ cat("\nTable formats are OK; enjoy your analyses!\n", sep="")
+
+ cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
+ format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+ cat("\n\n\n============================================================================")
+ cat("\nAdditional information about the call:\n")
+ cat("\n1) Parameters:\n")
+ print(cbind(value = argVc))
+
+ cat("\n2) Session Info:\n")
+ sessioninfo <- sessionInfo()
+ cat(sessioninfo$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$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+
+ cat("============================================================================\n")
+
+ sink()
+
+} else {
+
+ cat("\n\n\n============================================================================")
+ cat("\nAdditional information about the call:\n")
+ cat("\n1) Parameters:\n")
+ print(cbind(value = argVc))
+
+ cat("\n2) Session Info:\n")
+ sessioninfo <- sessionInfo()
+ cat(sessioninfo$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$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+
+ cat("============================================================================\n")
+
+ sink()
+ stop("Please check the generated 'information' file")
+
+}
+
+## closing
+##--------
+
+options(stringsAsFactors = strAsFacL)
+
+rm(list = ls())
diff -r 000000000000 -r 059eb452931e runit/.Rhistory
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/.Rhistory Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,1 @@
+q("no")
diff -r 000000000000 -r 059eb452931e runit/checkformat_runtests.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/checkformat_runtests.R Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,101 @@
+#!/usr/bin/env Rscript
+
+## Package
+##--------
+
+library(RUnit)
+
+## Constants
+##----------
+
+testOutDirC <- "output"
+argVc <- commandArgs(trailingOnly = FALSE)
+scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
+
+
+## Functions
+##-----------
+
+## Reading tables (matrix or data frame)
+readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
+
+ file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
+
+ switch(typeC,
+ matrix = return(t(as.matrix(read.table(file = fileC,
+ header = TRUE,
+ row.names = 1,
+ sep = "\t",
+ stringsAsFactors = FALSE)))),
+ dataframe = return(read.table(file = fileC,
+ header = TRUE,
+ row.names = 1,
+ sep = "\t",
+ stringsAsFactors = FALSE)))
+
+}
+
+## Call wrapper
+wrapperCallF <- function(paramLs) {
+
+ ## Set program path
+ wrapperPathC <- file.path(dirname(scriptPathC), "..", "checkformat_wrapper.R")
+
+ ## Set arguments
+ argLs <- NULL
+ for (parC in names(paramLs))
+ argLs <- c(argLs, parC, paramLs[[parC]])
+
+ ## Call
+ wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
+
+ if(.Platform$OS.type == "windows")
+ wrapperCallC <- paste("Rscript", wrapperCallC)
+
+ wrapperCodeN <- system(wrapperCallC)
+
+ if (wrapperCodeN != 0)
+ stop("Error when running checkformat_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[["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)
diff -r 000000000000 -r 059eb452931e runit/checkformat_tests.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/checkformat_tests.R Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,11 @@
+test_input_default <- function() {
+
+ testDirC <- "input"
+ argLs <- list()
+
+ argLs <- c(defaultArgF(testDirC), argLs)
+ outLs <- wrapperCallF(argLs)
+
+ checkEquals(outLs[['infVc']][4], 'Table formats are OK; enjoy your analyses!')
+
+}
diff -r 000000000000 -r 059eb452931e runit/input/dataMatrix.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/dataMatrix.tsv Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,4 @@
+dataMatrix 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 2569204.924 6222035.774 17070707.99 1258838.243 13039543.08 1909391.77 3495.093864 2293521.909 128503.2751 81872.52764 8103557.566 149574887 1544036.41 7103429.539 14138796.5 4970265.58 263054.7306 1671332.3 88433.1945 23602331.29 18648126.52 1554657.988 34152.36464 209372.7128 33187733.37 202438.5916 13581070.09 354170.8107 9120781.49 43419175.41
+HMDB03072 3628416.303 65626.98344 112170.1189 3261804.344 42228.27877 343254.2013 1958217.693 11983270.04 5932111.416 5511385.834 9154521.478 2632133.212 9500411.146 6551644.517 7204319.809 1273412.048 3260583.816 8932005.535 8340827.526 9256460.692 11217839.17 5919262.814 11790077.07 9567977.808 73717.58117 9991787.291 4208098.147 623970.6499 10904221.26 2171793.936
+HMDB00792 429568.6094 3887629.505 1330692.117 1367446.73 844197.4475 2948090.719 1614157.906 3740009.194 3292251.665 2310688.795 4404239.59 3043289.128 825736.4672 2523241.917 6030501.026 474901.6041 2885792.426 2955990.64 1917716.343 1767962.677 5926203.404 1639065.695 346810.7636 1054776.223 2390258.275 1831346.373 1026696.369 7079792.5 4368341.014 3495986.873
diff -r 000000000000 -r 059eb452931e runit/input/sampleMetadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/sampleMetadata.tsv Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,31 @@
+sampleMetadata age ageGrp
+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
diff -r 000000000000 -r 059eb452931e runit/input/variableMetadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/variableMetadata.tsv Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,4 @@
+variableMetadata name
+HMDB01032 Dehydroepiandrosterone sulfate
+HMDB03072 Quinic acid
+HMDB00792 Sebacic acid
diff -r 000000000000 -r 059eb452931e runit/output/information.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/information.txt Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,6 @@
+
+Start of the 'Check Format' Galaxy module call: Thu 04 Aug 2016 09:29:19 PM
+
+Table formats are OK; enjoy your analyses!
+
+End of the 'Check Format' Galaxy module call: Thu 04 Aug 2016 09:29:19 PM
diff -r 000000000000 -r 059eb452931e static/images/checkFormat_workflowPositionImage.png
Binary file static/images/checkFormat_workflowPositionImage.png has changed
diff -r 000000000000 -r 059eb452931e test-data/input-dataMatrix.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input-dataMatrix.tsv Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,4 @@
+dataMatrix 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 2569204.924 6222035.774 17070707.99 1258838.243 13039543.08 1909391.77 3495.093864 2293521.909 128503.2751 81872.52764 8103557.566 149574887 1544036.41 7103429.539 14138796.5 4970265.58 263054.7306 1671332.3 88433.1945 23602331.29 18648126.52 1554657.988 34152.36464 209372.7128 33187733.37 202438.5916 13581070.09 354170.8107 9120781.49 43419175.41
+HMDB03072 3628416.303 65626.98344 112170.1189 3261804.344 42228.27877 343254.2013 1958217.693 11983270.04 5932111.416 5511385.834 9154521.478 2632133.212 9500411.146 6551644.517 7204319.809 1273412.048 3260583.816 8932005.535 8340827.526 9256460.692 11217839.17 5919262.814 11790077.07 9567977.808 73717.58117 9991787.291 4208098.147 623970.6499 10904221.26 2171793.936
+HMDB00792 429568.6094 3887629.505 1330692.117 1367446.73 844197.4475 2948090.719 1614157.906 3740009.194 3292251.665 2310688.795 4404239.59 3043289.128 825736.4672 2523241.917 6030501.026 474901.6041 2885792.426 2955990.64 1917716.343 1767962.677 5926203.404 1639065.695 346810.7636 1054776.223 2390258.275 1831346.373 1026696.369 7079792.5 4368341.014 3495986.873
diff -r 000000000000 -r 059eb452931e test-data/input-sampleMetadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input-sampleMetadata.tsv Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,31 @@
+sampleMetadata age ageGrp
+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
diff -r 000000000000 -r 059eb452931e test-data/input-variableMetadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input-variableMetadata.tsv Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,4 @@
+variableMetadata name
+HMDB01032 Dehydroepiandrosterone sulfate
+HMDB03072 Quinic acid
+HMDB00792 Sebacic acid
diff -r 000000000000 -r 059eb452931e test-data/output-information.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output-information.txt Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,6 @@
+
+Start of the 'Check Format' Galaxy module call: Sat 30 Jul 2016 07:49:51 AM
+
+Table formats are OK; enjoy your analyses!
+
+End of the 'Check Format' Galaxy module call: Sat 30 Jul 2016 07:49:51 AM