tomas-pluskal
commented
8 years ago I was actually thinking about this. It is quite easy to add scripting to Java application through ScriptEngine class - the scripts can be written in Java, JavaScript, or even in Python (through Jython). The biggest difficulty here will be to provide enough documentation so people know how to actually write the scripts.
One way to do this is to provide a lot of example scripts so users can modify them. We can also add a function to export the commands executed in the GUI as a script.
PS: we have an issue for tracking the batch mode: #4
photocyte
Hi there,
It would be nice if there were a couple blocks for logic / flow control for batch mode.
An simple implementation might be to give the blocks an explicit integer order (e.g. 1,2,3,4,5). Then, there could be a logic block, which could GOTO a certain block if a condition is met (if raw file is all profile data or all positive mode scans etc.) Otherwise the batch would progress in an ascending order. Also it would be good if blocks could have the same order # (e.g. multiple chromatogram builders with order # 3), as then MZMine3 could execute things in parallel due to the existing modularity of the tasks.