Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-02-01 Thread Peter
Hi Kanewi,

Sorry - make that three changesets on this branch to consider
mering/transplanting:
https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31

Parameter handling,
https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063

Cope with errors on stderr,
https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c

Ensure blast jobs get killed,
https://bitbucket.org/peterjc/galaxy-central/changeset/607b7268693a

Peter
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev


Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-02-01 Thread Kanwei Li
Committed

On Tue, Feb 1, 2011 at 10:27 AM, Peter pe...@maubp.freeserve.co.uk wrote:
 Hi Kanewi,

 Sorry - make that three changesets on this branch to consider
 mering/transplanting:
 https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31

 Parameter handling,
 https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063

 Cope with errors on stderr,
 https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c

 Ensure blast jobs get killed,
 https://bitbucket.org/peterjc/galaxy-central/changeset/607b7268693a

 Peter

___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev


Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-01-05 Thread Daniel Blankenberg
Hi Peter,

The method to access additional fields from .loc files has been changed in 
4804:376cce23623d to be of the form:
${param.fields.path}.


Thanks again for your input,

Dan


On Jan 4, 2011, at 12:35 PM, Peter wrote:

 On Tue, Jan 4, 2011 at 2:26 AM, Daniel Blankenberg d...@bx.psu.edu wrote:
 Hi Peter (and -dev),
 
 Would something like ${param.fields.path} be preferred over
 ${param.get_fields( 'path' )}?
 
 Thanks,
 
 Dan
 
 That looks nicer to type in the XML wrapper, but I am not
 overly bothered. Could we use either syntax for things like
 filters and conditional checks (in other parameters)?
 
 Peter


___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev


Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-01-05 Thread Peter
On Wed, Jan 5, 2011 at 8:02 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
 Hi Peter,

 The method to access additional fields from .loc files has been changed in
 4804:376cce23623d to be of the form:
 ${param.fields.path}.


:)

Did you see Kanwei's email pointing out that while this is nice, it won't
work with special characters (e.g. hyphens), or another problem would
be reserved Python names (e.g. in)? I don't think this will be a problem
in practice, but should be touched on in the documentation for this
(and setting up loc files).

Peter
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev


Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-01-05 Thread Daniel Blankenberg
Hi Peter,

We had some discussion today about Kanwei's email and opted for the nicer 
looking access method. I've added a note to the ToolConfigSyntax wiki page 
about special characters.

Thanks,

Dan


On Jan 5, 2011, at 3:07 PM, Peter wrote:

 On Wed, Jan 5, 2011 at 8:02 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
 Hi Peter,
 
 The method to access additional fields from .loc files has been changed in
 4804:376cce23623d to be of the form:
 ${param.fields.path}.
 
 
 :)
 
 Did you see Kanwei's email pointing out that while this is nice, it won't
 work with special characters (e.g. hyphens), or another problem would
 be reserved Python names (e.g. in)? I don't think this will be a problem
 in practice, but should be touched on in the documentation for this
 (and setting up loc files).
 
 Peter


___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev


Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

2011-01-04 Thread Kanwei Li
I would think the get_fields way is more robust since you wouldn't run
into issues with special characters

On Tue, Jan 4, 2011 at 12:35 PM, Peter pe...@maubp.freeserve.co.uk wrote:
 On Tue, Jan 4, 2011 at 2:26 AM, Daniel Blankenberg d...@bx.psu.edu wrote:
 Hi Peter (and -dev),

 Would something like ${param.fields.path} be preferred over
 ${param.get_fields( 'path' )}?

 Thanks,

 Dan

 That looks nicer to type in the XML wrapper, but I am not
 overly bothered. Could we use either syntax for things like
 filters and conditional checks (in other parameters)?

 Peter
 ___
 galaxy-dev mailing list
 galaxy-dev@lists.bx.psu.edu
 http://lists.bx.psu.edu/listinfo/galaxy-dev

___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev