Galaxy

Galaxy servers as the main Graphical User Interface and framework for using the msCompare program in an easy and intuitive manner.
To install msCompare in galaxy download msCompare_For_Galaxy.tar.gz and follow the installation details in the README file.
Recent change to either the download package or nbic galaxy server (​http://galaxy.nbic.nl/) can be found here.

User Manual

General Data Processing Workflow in Galaxy

As of 13 Feb 2012 the default input format is mzML instead of mzXML.
(Figure not yet updated, everyoccurrence of mzXML in the figure should be read as mzML)

Galaxy Modules

Unfortunately not all modules are included at this moment in this list. However most other modules work similar to those explained in detail here.

LC-MS Data related

• create FileSet
• OpenMS PeakPicker?

Settings Related

• Get User Settings

Feature Quantification

• MZmine Feature Quantification
• OpenMS Feature Quantification

Feature Alignment & Matching

• MZmine Feature Matching
• OpenMS Feature Matching

Feature Matrix Related

• Export Feature Matrix
• Calculate the PeakMatrix Score

Example Server

NBIC is generously providing an "testing" server at which msCompare is hosted.
However at this location not all features of msCompare are installed.
The testing server can be found at: ​http://galaxy.nbic.nl/galaxy/

A small dataset available for testing with galaxy can be found at: ​http://galaxy.nbic.nl/galaxy/u/b-hoekman/h/example-dataset
The same dataset was processed (including statistics) the results can be found at: ​http://galaxy.nbic.nl/galaxy/u/b-hoekman/h/apml2