Hi all,

Something I've not needed to do until now is define a new file format
in Galaxy. I understand the basic principle and defining a subclass in
Python... however, how does this work with new tools on the Tool Shed?
In particular, if an output format is likely to be used by more than
one tool, can we get it added to the Galaxy core?

As an example, the basic functionality of the Blast2GO for pipelines
tool (b2g4pipe) takes a BLAST XML input file, and gives a tab
separated annotation output file. Galaxy already has 'blastxml' and
'tabular' file formats defined, so I didn't need to do anything extra.
However, the tool can also take (a directory of) InterProScan XML
files as input, so here a new 'interproscanxml' format would useful.
Then any wrapper using or producing InterProScan XML could take
advantage of this. e.g. Konrad's InterProScan wrapper could then offer
the XML output as an option in addition to or instead of the tabular

Related to this example, why isn't there a generic base class for XML
formats in general?


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