Comments (3)
Hi Greg,
Sorry for the delay. The -p
command expects a text file that is formatted like so (imzML expects coordinates to start at (1,1)):
1 1 1
2 1 1
3 1 1
where each line describes the coordinate (x, y, z) for scans in the mzML file in the order in which they appear. To skip a scan (if this is necessary) you can do (skipping the second scan:
1 1 1
-1 -1 -1
2 1 1
So I guess the quickest way to get up and running would be to write a script that parses the XML file and outputs a .txt file with the above format.
Perhaps a better (but longer term) solution would be to allow your XML file format as input in the -p
command. I'm not sure whether this is something you (or your group) would be interested in contributing?
Alan
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