Hello Bjoern, On Mar 9, 2013, at 5:26 AM, Björn Grüning wrote:
Hi all!
I'd like to define 'blastxml' to 'tabular' conversion within Galaxy so that this can be used automatically (e.g. Tools expecting just tabular data would have converted BLAST XML files listed in the drop down). The functionality to do this exists in my Python tool 'blastxml_to_tabular' currently in the 'ncbi_blast_plus' repository, which might have to move into 'blast_datatypes' for this to work. http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
I've skimmed over the instructions here, but would like to look at a couple of real examples to make sure I've understood: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013434.html
Are there any good examples of 3rd party Galaxy datatypes defining conversion like this?
To add some more question to that topic. How to hide the converter from the tool-panel, when its available within Galaxy?
This is a known issues, and there is a Trello card for it here. I'll be working on this issues this week and the fix should be included in the next Galaxy release. https://trello.com/card/toolshed-fix-the-process-that-currently-adds-entries...
And is it possible to use third-party tool-shed dependencies in data-type definition files? I have a data-type that is really hard to sniff. I would like to use an external library for that purpose.
Including tool dependency definitions inside datatype_conf.xml files is not supported. Can you clarify this a bit? It would be good to get some details of the specific components you're dealing with so I can get a clear picture of what may be required here.
Thanks, Bjoern
Thanks! Greg Von Kuster
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