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-to-the-galaxy-tool-panel/506338ce32ae458f6d15e4b3/642 > 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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
