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peterjc / galaxy_blast

Galaxy wrappers for NCBI BLAST+ and related BLAST tools.
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Skip query hits above user-defined threshold #147

Open nuno-agostinho opened 2 years ago

nuno-agostinho commented 2 years ago

Hello, thanks for writing blastxml_to_tabular.py!

It does almost everything I need. However, as I only care about the top hits, I added an option to filter the number of hits returned based on Hit_num from the XML input file (by default, nothing is filtered).

I opened this PR in case you find that these changes may be helpful to other users.

Best regards, Nuno

peterjc commented 2 years ago

Interesting - it reminds me of how I used to use https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr but yours is more general.

I feel this could be the start of a slippery slope, morphing from XML to tabular conversion, into BLAST result filtering. It might be better to implement a separate BLAST filtering tool? But then which format(s) would you want to be able to filter?

Hmm. Either way, I've not been using Galaxy recently and really need to look at #140 before risking any non-trivial update to the wrappers.