workflow4metabolomics / biosigner

Discovery of significant signatures from omics data

Discovery of significant signatures from omics data

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 2.2.6
Date: 2016-08-05
Author: Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
Email: etienne.thevenot(at)cea.fr
Citation: Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2015). biosigner: A new method for the discovery of restricted and stable molecular signatures from omics data. Frontiers in Molecular Biosciences, in review.
Licence: CeCILL Reference history: W4M00003_diaplasma
Funding: Agence Nationale de la Recherche (MetaboHUB national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)

Installation

• Configuration file: biosigner_config.xml
• Image files:
  • static/images/biosigner_workflowPositionImage.png
  • static/images/biosigner_workingExampleImage.png
• Wrapper file: biosigner_wrapper.R
• R packages

• batch from CRAN

  install.packages("batch", dep=TRUE)  

• biosigner from Bioconductor

  source("http://www.bioconductor.org/biocLite.R")  
  biocLite("biosigner")

Tests

The code in the wrapper can be tested by running the runit/biosigner_runtests.R R file

You will need to install RUnit package in order to make it run:

install.packages('RUnit', dependencies = TRUE)

Working example

See the W4M00001a_sacurine-subset-statistics or W4M00003_diaplasma shared histories in the Shared Data/Published Histories menu (https://galaxy.workflow4metabolomics.org/history/list_published)

News

CHANGES IN VERSION 2.2.6

INTERNAL MODIFICATION

• Minor internal modifications

CHANGES IN VERSION 2.2.4

INTERNAL MODIFICATION

• Internal updates for planemo and travis validation

CHANGES IN VERSION 2.2.2

INTERNAL MODIFICATION

• Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3)

CHANGES IN VERSION 2.2.1

NEW FEATURE

• Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)

biosigner's Issues

Failure while processing new mtbls404 files

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 1 did not have 79 elements
Calls: read.table -> scan
Execution halted

See phnmnl/container-galaxy-k8s-runtime#269

Test failure

The script test/test-biosigner fails in branch develop.
The file test-data/variableMetadata.out is different from the one obtained. The value svm in the last column has disappeared.
Needs quick correction in develop branch for PhenoMeNal Dalcotidine release.

22c22
< 3,7-Dimethyluric acid 1       HMDB01982       AroHeP  svm
---
> 3,7-Dimethyluric acid 1       HMDB01982       AroHeP
32,33c32,33
< Acetaminophen glucuronide     1       HMDB10316       Carboh  svm
< Acetylphenylalanine   1       HMDB00512       AA-pep  plsda|svm
---
> Acetaminophen glucuronide     1       HMDB10316       Carboh
> Acetylphenylalanine   1       HMDB00512       AA-pep  plsda
78,79c78,79
< N2-Acetylaminoadipic acid     2               AA-pep  svm
< N4-Acetylcytidine     1       HMDB05923       Nucleo  svm
---
> N2-Acetylaminoadipic acid     2               AA-pep
> N4-Acetylcytidine     1       HMDB05923       Nucleo
87c87
< Pantothenic acid      1       HMDB00210       AliAcy  plsda|svm
---
> Pantothenic acid      1       HMDB00210       AliAcy  plsda
95c95
< Pyrroledicarboxylic acid      2               AroHeM  svm
---
> Pyrroledicarboxylic acid      2               AroHeM

Pictures not displayed in help section

Workflow position picture and Output figure are not displayed in the help section.

fix versions

I think it would be better to fix the versions of the dependencies:

biosigner/biosigner_config.xml

Line 4 in ad64042

<requirements>

Fix tests

The test fails but return a green light.
@pkrog or @ethevenot can you fix that?

Fix planemo test

Planemo test is broken.