Peter Cock
It would be great to offer some way of displaying BLAST output (ideally at least BLAST XML and tabular) using the Galaxy Visualizations framework (Goecks et al. 2013).
I've just hit the following problem with BLAST+ 2.2.29 writing these warning messages to stderr which (sadly) start with `Error:` and so match our regex: ``` Error: (1431.1) FASTA-Reader: Warning:...
See email and proposed solution from Thomas Berner on the galaxy-dev list http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-June/015103.html He suggested adding a new `taxid_name.loc` file, e.g. $ more taxid_name.loc Hordeum vulgare 4513 Oryza sativa 4530...
It would be very useful to include tests for blastn etc using a BLAST database as from the user's history. This may require first supporting uploading a BLAST database into...
Filing an overdue issue for this previously discussed enhancement. See early work by @jj-umn as part of Galaxy-P on this branch (checked in by @jmchilton): https://bitbucket.org/galaxyp/galaxyp-toolshed-blast/commits/branch/default Using `-remote` makes several...
There is probably enough duplication between these three tools to justify some new macros...
See also #24 to wrap convert2blastmask, and #25 to wrap segmasker - dustmasker is done
TODO - How to handle the dependency on the cdd_delta database? A new loc file?
This might solve #18, but at the cost of hiding some true misuse of italics or bold within the same docstring. Might be worthwhile all the same? (This is a...