biocontainers/mzml2isa repository overview

⁠mzml2isa

Version: 1.0.0

⁠Short Description

A container image definition for the mzml2isa python tool

⁠Description

mzml2isa is a Python3 program that can automatically generate ISA-Tab document structure metadata files from raw XML metabolomics data files (mzML open access data format). The mzml2ISA tool provides the backbone of ISA-Tab metabolomics study which can then be edited with an ISA editing tool, ISAcreator.

⁠Key features

• Extract meta information from mzML files and stores it as either python dictionary or JSON format
• Creates an ISA-Tab file structure with relevant meta information filled in.
• Add additional metadata that cannot be parsed from mzML files to the ISA-Tab files through a JSON formatted dictionnary.

⁠Functionality

• Other Tools

⁠Approaches

⁠Instrument Data Types

⁠Tool Authors

• Martin Larralde

⁠Container Contributors

• Pablo Moreno⁠ (EMBL-EBI)

⁠Website

• https://github.com/ISA-tools/mzml2isa⁠

⁠Git Repository

• https://github.com/phnmnl/container-mzml2isa.git⁠

⁠Installation

For local individual installation:

docker pull docker-registry.phenomenal-h2020.eu/phnmnl/mzml2isa

⁠Usage Instructions

For direct docker usage:

docker run docker-registry.phenomenal-h2020.eu/phnmnl/mzml2isa ...

⁠Publications

• Rocca-Serra, P., Brandizi, M., Maguire, E., Sklyar, N., Taylor, C., Begley, K., ... & Neumann, S. (2010). ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics, 26(18), 2354-2356.