Hi Katherine:
This is outside my experience… but I wonder if you could try using a formulaic
name for the output (output1, output2, output3, output4) rather than base the
output name on the input file’s name.
Maybe someone else has some experience with something like this?
Brad
—
Brad Langhor
Hmm, unfortunately the paths have to be dynamically generated because this
is basically just an upload tool, but for another filesystem on your
computer other than the default (like Finder for Mac for example), in my
case 'iRODS', so its not really feasible to have something like a file
browser or
Hi:
Yes - let’s say you have hard coded paths… you could put those into a select
list pretty easily (just have the paths embedded like the bowtie wrapper does
the paired-end vs. single-end select list).
You might also want to consider a table lookup though.
The bowtie wrapper does that for ref
Hi Brad,
So with multiple selection dropdown lists this is possible? Do you have an
example of a tool that can do this? Would it be possible to see an example
of the tools you are talking about? Thanks for the help!
Katherine
On Fri, Aug 26, 2016 at 12:05 PM, Langhorst, Brad wrote:
> Hi Katherin
Hi Katherine:
I’d recommend not having users type in paths if at all possible (they will make
frustrating mistakes).
If there is a selection of these maybe consider turining them into dropdown
lists.
Either way, these would be no different than e.g. user specified downsampling
amounts. or li
Hi Brad,
What if its multiple file paths that the user types in rather than actual
files, which makes it so the tool can't be executed in batch mode, would it
still be workflow compatible at that point? Thanks for pointing me to the
Bowtie wrappers as an example.
Katherine
On Fri, Aug 26, 2016 at
HI Katherine:
Multi-input/output should work fine…
You could have a look at the bowtie wrappers for an example.
It takes up to 2 fastq files and a reference. I can output a few files
(unmapped, mapped, etc)
Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs
On Aug 26,
On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Peter,
> I think I did not explain myself well. I meant that if I have a tool that
> takes multiple file paths and outputs multiple Galaxy datasets to the
> history, would this tool be workflow comp
Hi Katherine,
Are you asking about compatibility staying on the same Galaxy
instance, or the harder problem of compatibility sharing workflows
between Galaxy servers?
Taking data from input Galaxy datasets should be fine, anything else
may not be portable. Even the relatively simple case of using
Hi Everyone,
Would anyone be able to tell me the conditions which would make a tool
non-workflow compatible? I have a tool that imports files from a third
party application and auto-detects the file format. There is also the
option to upload multiple files at once so the tool always uploads at leas
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