On Tue, Jul 30, 2013 at 4:29 PM, Shafer, Christina
<csha...@morgridgeinstitute.org> wrote:
> My question is related to this post in the archive. As recommended, I
> referred to
> http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
> for some guidance on how to achieve multiple output files, specifically one
> set of six files per number of times the <repeat> tag is called. The example
> provided isn't that informative, however, as it doesn't show what the
> example_tool.sh command script is doing so I can make my perl wrapper script
> do the same thing. If I have six files total, do I only specify one in the
> <outputs> tag and then have the remaining 5 named according to the scheme in
> the perl wrapper? Or is it Galaxy that does the naming of the remaining
> files automatically? Is there a perl equivalent to the "$__new_file_path__"
> variable that I can use, or is this the literal resolved file path (e.g.
> "/opt/galaxy/... etc)?
> Right now, upon execution of my tool, if a user has two entries (so number
> of times <repeat> has executed is twice), my perl wrapper is called twice
> (good), but on the second call, Galaxy uses the same output filenames as the
> first run such that the first set of output files are all overwritten by the
> second execution (bad). How do I make sure that each <repeat> iteration
> results in a unique set of output files?

The normal expectation is the Galaxy wrapper calls the tool ONCE only,
with a more complex command line including multiple file names from
the repeat.

If I recall correctly from your last email, you are using a trick with semi
colons to embed multiple shell commands in the <command> tag, one
for each repetition of the <repeat> tag.

I suggest you rework your Perl script to be designed to be called once
for all the work,

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