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ISA-tools / mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure
GNU General Public License v3.0
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Platform fix #28

Closed Tomnl closed 7 years ago

Tomnl commented 7 years ago

Fix for issue #27

"Platform" not recorded properly in the Investigation file.

Problem occurs when user has have both positive and negative mzML and the user has selected to split the mzML files into 2 assays (1 for pos and 1 for neg).

To solve this I have added as small fix that checks if positive and negative files should be separated into different assays. If this is true then I simply store two "Platform" names accordingly in the investigation file. (The "Platform" name is set as the instrument name derived from the mzML files)

NOTE: If there are multiple mzML files with different instrument names (e.g. Q-Exactive, LTQ Orbitrap) then a warning is given to check the "Platform" is recorded properly. The platform will be recorded as a combination of both instruments e.g ("Q-Exactive, LTQ Orbitrap") in these cases.

I think this is an unlikely occurrence anyway as in most cases I imagine it is one instrument name per assay.

Tomnl commented 7 years ago

@althonos, Will squash and merge tomorrow morning if the changes seem OK to you