Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-08-15 Thread Nate Coraor
Peter Cock wrote: On Fri, Jun 3, 2011 at 10:03 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks for the link - I was aware my initial work on adding a generic XML filetype was missing some steps, but I ran out of time yesterday: https://bitbucket.org/galaxy/galaxy-central/issue/568

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-08-15 Thread Peter Cock
On Mon, Aug 15, 2011 at 6:33 PM, Nate Coraor n...@bx.psu.edu wrote: Peter Cock wrote: On Fri, Jun 3, 2011 at 10:03 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks for the link - I was aware my initial work on adding a generic XML filetype was missing some steps, but I ran out of

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-08-10 Thread Peter Cock
On Fri, Jun 3, 2011 at 10:03 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks for the link - I was aware my initial work on adding a generic XML filetype was missing some steps, but I ran out of time yesterday: https://bitbucket.org/galaxy/galaxy-central/issue/568 Hi all, Could someone

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-06-09 Thread Greg Von Kuster
Hi Peter, On Jun 9, 2011, at 12:02 PM, Peter Cock wrote: Is there anything documented about the built-in format conversion within the Galaxy core, rather than tools. No, not currently - except for a few details in various slide presentations. Nothing forma though. We're trying to

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-06-06 Thread Peter Cock
On Thu, Jun 2, 2011 at 6:39 PM, Greg Von Kuster g...@bx.psu.edu wrote: We will certainly include support for new data formats into the Galaxy core.  In case you haven't seen it, details for adding new formats is available in our wiki at

[galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-06-02 Thread Peter Cock
Hi all, Something I've not needed to do until now is define a new file format in Galaxy. I understand the basic principle and defining a subclass in Python... however, how does this work with new tools on the Tool Shed? In particular, if an output format is likely to be used by more than one

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-06-02 Thread Greg Von Kuster
On Jun 2, 2011, at 1:29 PM, Nate Coraor wrote: Peter Cock wrote: Hi all, Something I've not needed to do until now is define a new file format in Galaxy. I understand the basic principle and defining a subclass in Python... however, how does this work with new tools on the Tool Shed? In