Re: [galaxy-dev] Output files using format="input"
On Wed, Dec 15, 2010 at 9:08 PM, James Taylor <james@jamestaylor.org> wrote:
Excerpts from Peter's message of Wed Dec 15 17:18:05 +0000 2010:
Is there some undocumented trick like format="input:paramname" where you can specify the input parameter name?
No, but that is a great idea.
:-) In the meantime, I think I can workaround this for a short list of known formats using <change_format>, akin to the way the wrapper fastq/fastq_combiner.xml maps the FASTA and QUAL input file formats to the FASTQ output variant. Peter
See here for a patch: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003013.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003014.html Peter wrote, On 12/16/2010 12:08 PM:
On Wed, Dec 15, 2010 at 9:08 PM, James Taylor <james@jamestaylor.org> wrote:
Excerpts from Peter's message of Wed Dec 15 17:18:05 +0000 2010:
Is there some undocumented trick like format="input:paramname" where you can specify the input parameter name?
No, but that is a great idea.
:-)
In the meantime, I think I can workaround this for a short list of known formats using <change_format>, akin to the way the wrapper fastq/fastq_combiner.xml maps the FASTA and QUAL input file formats to the FASTQ output variant.
Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On Thu, Dec 16, 2010 at 5:13 PM, Assaf Gordon <gordon@cshl.edu> wrote:
See here for a patch: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003013.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003014.html
Great to see you had the same idea for the naming... or maybe I'd read your email a while ago and (almost) forgotten it? ;) Do you know if your patch is still good, or if it needs updating? Could you put it up as a changeset on bitbucket? Given the positive response from James earlier I'd hope it could be merged into the trunk after testing. In your email you said "I guess it's not very a common scenario", well I think the example of FASTQ files (and also tabular files?) which both come in several subtypes contradicts that. This seems like a limitation worth fixing. Peter
Peter, Peter wrote, On 12/16/2010 12:24 PM:
On Thu, Dec 16, 2010 at 5:13 PM, Assaf Gordon <gordon@cshl.edu> wrote:
See here for a patch: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003013.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003014.html
Do you know if your patch is still good, or if it needs updating?
The patch to "lib/galaxy/tools/actions/__init__.py" is OK ( http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003013.html ) The patch to the javascript won't work, here's an updated patch. Note that: 1. I didn't test this updated version yet. 2. If you manually patch the javascript file (not waiting for the galaxy team), you'll have to copy it to (and overwrite) the "packed" version in ./static/scripts/packed/galaxy.workflow_editor.canvas.js , or re-pack it yourself . -gordon
On Wed, Dec 22, 2010 at 10:55 PM, Assaf Gordon <gordon@cshl.edu> wrote:
Peter,
Peter wrote, On 12/16/2010 12:24 PM:
On Thu, Dec 16, 2010 at 5:13 PM, Assaf Gordon <gordon@cshl.edu> wrote:
See here for a patch: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003013.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003014.html
Do you know if your patch is still good, or if it needs updating?
The patch to "lib/galaxy/tools/actions/__init__.py" is OK ( http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/003013.html )
The patch to the javascript won't work, here's an updated patch.
Note that: 1. I didn't test this updated version yet. 2. If you manually patch the javascript file (not waiting for the galaxy team), you'll have to copy it to (and overwrite) the "packed" version in ./static/scripts/packed/galaxy.workflow_editor.canvas.js , or re-pack it yourself .
-gordon
Hi, I haven't dug into the code, but why would you need to touch the Javascript? Surely this can all be done in Python on the server side? Peter
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