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A cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with spectrum filtering capabilities.
ExfilMS is a cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with spectrum filtering capabilities.
ExfilMS has been tested on Windows, macOS and Linux.
[!IMPORTANT]
Prerequisite: Node.js®
$ npm i -g exfilms
[!IMPORTANT]
Prerequisite: Docker
# Clone repository
$ git clone https://github.com/vmalnathnambiar/exfilms.git
# Navigate into repository
$ cd exfilms
# Build Docker image
$ docker build -t exfilms .
# Using command line arguments
$ exfilms -i "/path/to/input/directory/containing/mzML/data/files/" ...
# Interactive
$ exfilms -x
# Using command line arguments
$ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -i /inputDirectory -o /outputDirectory -l /logDirectory ....
# Interactive
$ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -x
[!NOTE]
Running ExfilMS using Docker requires the use of volume mapping in the Docker command. For example,
-v "/path/on/the/local/machine/":/tmpPath
Once the volume mapping is done, you would use /tmpPath as the input data where required, instead of the actual path on the local machine. For the successful execution of ExfilMS, you are REQUIRED to provide the following:
- -v "/path/to/input/directory/":/inputDirectory
- -v "/path/to/output/directory/":/outputDirectory
- -v "/path/to/log/directory/":/logDirectory
For more guidance on how to use ExfilMS, please refer to our available guides below:
[!WARNING]
- Unable to extract MS data from Bruker EVOQ instruments (unsupported format by ProteoWizard).
- Unable to parse mzML data that has a file size GREATER THAN 2GB.
- Large MS data may cause Node environment to terminate abruptly due to memory limit exhaustion.
- Slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.
- Unable to output extracted files when running ExfilMS in interactive mode with Docker.
If you use ExfilMS in your work, please cite it using the following:
Nambiar, V. (2024). ExfilMS. GitHub. https://github.com/vmalnathnambiar/exfilms
Please refer to our license information here.
FAQs
A cross-platform, command line interface tool to extract mass spectrometry data from mzML formatted files, with filtering capabilities.
The npm package exfilms receives a total of 0 weekly downloads. As such, exfilms popularity was classified as not popular.
We found that exfilms demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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