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zamboni-lab / SLAW

Scalable and self-optimizing processing workflow for untargeted LC-MS
GNU General Public License v2.0
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ADAP Batch File Empty #14

Closed bmgarcia closed 2 years ago

bmgarcia commented 2 years ago

Hello,

When trying to import the batch file created by SLAW into MZmine I get the following readback from MZmine "Loaded 0 batch step(s) from batch_xml_adap.xml".

Is there a different way of importing this? I can see the data is retained for each step in the .xml file when opening in a text editor, but for some reason I can't get it to import into MZmine.

Thanks.

htmonkey commented 2 years ago

The reason is that the method in the XML file are not recognized by the mzMine you are using to load it. This is because the method class names in mzMine can change between versions and there is no backward compatibility. As SLAW wraps mzMine v 2.52, you should use the same version to load batch files directly.

Alternatively, you have to update the method names in the "batch_xml_adap.xml" file to match the mzMine version you are currently using. For example, <batchstep method="net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule"> should be replaced by e.g. <batchstep method="io.github.mzmine.modules.io.rawdataimport.RawDataImportModule"> and so on...

Quite tedious, but blame it on mzMine ;-)