Galaxy | Tool Preview

NMR_Read (version 3.3.0)
Default value is line 1
Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories
Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)

Authors Manon Martin (manon.martin@uclouvain.be) and Marie Tremblay-Franco (marie.tremblay-franco@inra.fr; Galaxy integration)

Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.

NMR Read

Description

Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR))

Workflow position

Upstream tools

Name output file format
NA NA NA

Downstream tools

Name Output file Format
NMR_Preprocessing dataMatrix Tabular
NMR_Preprocessing sampleMetadata Tabular
NMR_Preprocessing NMR_Read_log TXT
NMR_Preprocessing NMR_Read_graph PDF
NMR_Alignement dataMatrix Tabular
NMR_Bucketing dataMatrix Tabular
Normalization dataMatrix Tabular
Univariate variableMetadata Tabular
Multivariate sampleMetadata Tabular
  variableMetadata Tabular

Input files

Parameter : num + label Format
1 : Choose your inputs zip

Choose your inputs

Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip.

Parameters

FID Title line
Line in the acqus file to find the FID title (name)

subdirectories
Organization of individual's files
TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.

dirs_names
Use the (sub)directories names as FID names?

Output files

NMR_Read_dataMatrix
tabular output
Data matrix with n rows (samples) and p columns (time) containing the raw FIDs.

NMR_Read_sampleMetadata
tabular output
Data matrix with n rows (samples) containing the acquisition parameters for each sample.

NMR_Read_log
Text output
Contains warnings

NMR_Read_graph
pdf output
line plots of FID

Creating the zip file

Must contain at least the following files for every sample: fid, acqu and acqus

/repository/static/images/77d77e9ed22c8547/.%2Fstatic%2Fimages%2FReadFids.png

Possible structure and parameters values:

  1. use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE, dirs_names = FALSE
  2. use title file and no sub-directories: set the FID Title line, subdirectories = FALSE, dirs_names = FALSE
  3. don't use title file and presence of sub-directories: subdirectories = TRUE, dirs_names = TRUE
  4. don't use title file and no sub-directories: subdirectories = FALSE, dirs_names = TRUE

Changelog/News

Version 3.3.0

  • Debugged R scripts for possibly negative baselines

Version 3.2.0

  • Updated R scripts and the help section of NMR_ReadFids and NMR_preprocessing
  • Added sections
  • Created a variableMetadata file in output of the NMR_preprocessing module
  • Homogenised the input-output file names with the other modules
  • Suppressed the option ptw for the baseline correction, set to TRUE all the time now
  • Shift referencing: other values than 0 are admitted
  • The log file recovers the input/output parameters
  • Added an exclusion zone for the computation of the Baseline Correction criterion
  • Switched Internal Referencing (goes second) and Zero Order Phase Correction (goes first)

Version 3.1.0

  • Implementation of NMR_ReadFids and NMR_preprocessing