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 to hard code the paths.

Although I do have a dynamic select list working at the moment and do get
multiple files outputted into my history, when I try to use one of the
files I uploaded, in a workflow, I get this error:

File '/home/katie/galaxy/lib/galaxy/workflow/run.py', line 308 in
replacement_for_connection

  raise Exception( message )

Exception: Workflow evaluation problem - failed to find output_name
__new_primary_file_output|foo.txt__ in step_outputs {'output':
<galaxy.model.HistoryDatasetAssociation object at 0x7f976ecbb410>}

And when I look in the database (table workflow_step_connection) every
other normal file's output_name is the name of the output variable from the
tool config file, for example if the parameter is <output name=output1...
then that is the output_name for the file resulting from that tool
execution. So why is it giving me something strange like
__new_primary_file_output|foo.txt__ when the file comes from a tool
execution where multiple files were outputted to the history.

Katherine

On Fri, Aug 26, 2016 at 2:22 PM, Langhorst, Brad <langho...@neb.com> wrote:

> 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 reference genomes.
> You can make your own lookup table to refer to whatever files you want,
> which would allow you to update paths without installing new version of the
> tool.
>
>
>
> brad
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Aug 26, 2016, at 1:06 PM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
> 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 <langho...@neb.com>
> wrote:
>
>> 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 library names, etc.
>> I have tools that accept many of these.
>>
>>
>> Brad
>>
>> —
>> Brad Langhorst, Ph.D.
>> Development Scientist
>> New England Biolabs
>>
>>
>>
>>
>> On Aug 26, 2016, at 10:57 AM, Katherine Beaulieu <
>> katherine.beaulieu...@gmail.com> wrote:
>>
>> 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.
>>
>>
>>
>
>
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