Hi all,
In biology we often want to use italics, the key examples
that come to mind are species and gene names. I think
it is natural therefore to want to be able to use italics in
the description of data resources in Galaxy's loc files.
For example, in our local Galaxy for the BLAST databases
listed in blastdb.loc and blastdb_p.loc, I currently have
some <i>Species name</i> entries (using the HTML i
tag for italics).
[I originally compiled our BLASTDB loc files from our
existing configuration files for wwwblast, where the
HTML italics tags worked.]
In the Galaxy BLAST+ tools, the select database
parameter field shows these entries in plain text (with
no italics styling, and without the HTML tags). I'm not
confident about this looking back, but would this ever
have shown the italics? It would be nice if it did...
Is this sanitation (removing the tags) deliberate?
This brings me to my next question - I'm working on
a wrapper for the NCBI BLAST+ tool blastdbcmd,
and setup the output file as follows in the tool XML:
<outputs>
<data name="seq" format="fasta"
label="Sequences from ${db_opts.database.fields.name}" />
</outputs>
This works, but in the right hand history panel, the dataset
name is shown with the raw HTML tags from the loc file (in
this case when I have a species specific BLAST database,
the user sees the < i > and < /i > tags around the species
name).
So, there is an inconsistency: The select parameter seems
to sanitize the tags, the output label does not.
Ideally I would like both to support italics and bold, but
would settle on both being sanitised.
If this is not intended to work, I'll just remove the italics
tags from our BLAST loc files.
If this is intended to work, should I file an issue on bitbucket?
Thanks,
Peter
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