Available Fragment Commands
To get a list of available commands, you can query maltcms directly:
>maltcms.sh -l cross.commands.fragments.AFragmentCommand
To find out about the parameters supported by an individual command:
>maltcms.sh -s maltcms.commands.fragments.peakfinding.TICPeakFinder
If you want to generate a basic configuration file for a number of commands:
>maltcms.sh -b maltcms.commands.fragments.peakfinding.TICPeakFinder
You can provide multiple commands by separating them with a ‘,’. The created pipeline will be in the ‘maltcmsOutput/pipelines/’ directory below the current working directory. The created files are just a starting point and will most probably not work immediately. For hints on completing the configuration files, please consult the provided pipelines below ‘cfg/pipelines/’ and ‘cfg/pipelines/xml’.
If you have further questions, please feel free to contact the author. Currently, the following fragment commands are available for execution within the pipeline:
These pages also give detailed information about the user-definable properties that are supported by each command.