Sharing tool definitions between XML files
Hi all, I'm wondering if there is any established way to share parameter definitions between tool wrapper XML files? For example, I am currently working on NCBI BLAST+ wrappers, and these tools have a lot in common. For example, the output format option will be a select parameter, and it will be the same for blastn, blastp, tblastn, etc. I can just cut and paste the definition but this seems inelegant and will be a long term maintenance burden if it ever needs updating (lots of places would need to be updated the same way). I'd like to have a shared XML snippet defining this parameter which I could then reference/include from each tool wrapper than needs it. I'm thinking of something like XML's <!ENTITY ...> might work. Is this possible? Peter
On Tue, Sep 28, 2010 at 12:04 PM, Peter <peter@maubp.freeserve.co.uk> wrote:
Hi all,
I'm wondering if there is any established way to share parameter definitions between tool wrapper XML files?
For example, I am currently working on NCBI BLAST+ wrappers, and these tools have a lot in common. For example, the output format option will be a select parameter, and it will be the same for blastn, blastp, tblastn, etc. I can just cut and paste the definition but this seems inelegant and will be a long term maintenance burden if it ever needs updating (lots of places would need to be updated the same way). I'd like to have a shared XML snippet defining this parameter which I could then reference/include from each tool wrapper than needs it.
I'm thinking of something like XML's <!ENTITY ...> might work. Is this possible?
Peter
Alex Bossers replied on the BLAST+ thread to express interest in sharing definitions between wrapper XML files: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003376.html As I add more parameters to my BLAST+ wrappers, keeping all the files in sync is getting a bit tedious... Peter
On Wed, Oct 6, 2010 at 11:16 AM, Peter <peter@maubp.freeserve.co.uk> wrote:
On Tue, Sep 28, 2010 at 12:04 PM, Peter <peter@maubp.freeserve.co.uk> wrote:
Hi all,
I'm wondering if there is any established way to share parameter definitions between tool wrapper XML files?
For example, I am currently working on NCBI BLAST+ wrappers, and these tools have a lot in common. For example, the output format option will be a select parameter, and it will be the same for blastn, blastp, tblastn, etc. I can just cut and paste the definition but this seems inelegant and will be a long term maintenance burden if it ever needs updating (lots of places would need to be updated the same way). I'd like to have a shared XML snippet defining this parameter which I could then reference/include from each tool wrapper than needs it.
I'm thinking of something like XML's <!ENTITY ...> might work. Is this possible?
Peter
Alex Bossers replied on the BLAST+ thread to express interest in sharing definitions between wrapper XML files:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003376.html
As I add more parameters to my BLAST+ wrappers, keeping all the files in sync is getting a bit tedious...
Peter
Hi all, I'm replying to this old thread after finding this old (fixed) issue on the bug tracker, https://bitbucket.org/galaxy/galaxy-central/issue/131/allow-xml-includes-in-... Does this offer a solution to sharing definitions in tool XML files? Has anyone got an example using this? Peter
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