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,

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,

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

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

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

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