workflow4metabolomics/checkformat

Name: checkformat

Owner: Workflow4Metabolomics

Description: Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files

Created: 2016-07-30 14:03:23.0

Updated: 2016-07-30 14:04:25.0

Pushed: 2018-01-11 17:11:48.0

Homepage: null

Size: 682

Language: R

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README

Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 3.0.0
Date: 2018-01-10
Author: Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
Email: etienne.thevenot(at)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
Licence: CeCILL
Reference histories:
W4M00001a_sacurine-subset-statistics, W4M00001b_sacurine_complete, W4M00002_sacurine_mtbls2, W4M00003_sacurine_diaplasma
Funding: Agence Nationale de la Recherche (MetaboHUB 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

  all.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:

all.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 3.0.0

NEW FEATURES

• Automated re-ordering (if necessary) of sample and/or variable names from dataMatrix based on sampleMetadata and variableMetadata
  

• New argument to make sample and variable names syntactically valid
  

• Output of dataMatrix, sampleMetadata, and variableMetadata files, whether they have been modified or not
  

CHANGES IN VERSION 2.0.4

INTERNAL MODIFICATION

• Minor internal modifications
  

CHANGES IN VERSION 2.0.2

INTERNAL MODIFICATION

• Creating tests for R code