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phnmnl / container-galaxy-k8s-runtime

PhenoMeNal runtime for Galaxy running inside a container orchestrator
Apache License 2.0
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Reference to undefined `raw` data format #213

Closed ilveroluca closed 6 years ago

ilveroluca commented 6 years ago

The phenomenal/ms/dimspy/process_scans.xml wrapper is referencing a data format/extension called raw that isn't defined in Galaxy. The start-up logs show this warning:

galaxy.tools.parameters.basic WARNING 2018-06-20 17:40:17,617 Datatype class not found for extension 'raw', which is used in the 'format' attribute of parameter 'source'

The references are on lines 94 and 99 of the wrapper file.

jbradbury commented 6 years ago

@ilveroluca as far as I am aware (I am no expert with dimspy) raw files from some manufacturers can be used with dimspy process scans

jbradbury commented 6 years ago

@ilveroluca on Galaxy the data type is called thermo.raw

ilveroluca commented 6 years ago

Then PR #286 should be good for approval. It removes the reference to raw while leaving unchanged the references to thermo.raw and mzml.