Yes, I'm sure that's where the problem lies. Writing out to the current
directory doesn't work.  The files get written to
'job_working_directory/000/1/' but if I run the Upload File tool the result
is placed in 'files/000/'.  I think I need to work out where to write the
files, I found some references to $__new_file_path__ but that doesn't seem
to help.

Steve



On 20 October 2015 at 19:57, Peter van Heusden <p...@sanbi.ac.za> wrote:

> I suspect that the problem might be in the <discover_datasets> then. I'm
> not an export on this, but "__name_and_ext__" turns into the
> regexp r"(?P<name>.*)\.(?P<ext>[^\.]+)?" in
> lib/galaxy/tools/parameters/output_collect.py, and is used by the
> DatasetCollector (line 358). This looks like it should match the filenames
> you're creating, but I'm not 100% sure how that code works. One thing I
> notice is the "directory" argument. If you write jobs to the current
> directory instead of "output_path" can you get it to work?
>
> Peter
>
> On 20 October 2015 at 09:52, Steve Cassidy <steve.cass...@mq.edu.au>
> wrote:
>
>> Thanks Peter,
>>   I did see that proviso somewhere but no, refreshing doesn't help.
>>
>> That page was one of those that I referred to getting to this point.
>>
>> Steve
>>
>> On 20 October 2015 at 18:33, Peter van Heusden <p...@sanbi.ac.za> wrote:
>>
>>> Just a quick check - did you refresh your history to confirm that the
>>> dataset *is* empty? We had the same thing at SANBI but it turns out that
>>> Galaxy creates an empty output collection and then only populates it
>>> sometime after job completion (this is a know UI bug).
>>>
>>> See:
>>> http://pvh.wp.sanbi.ac.za/2015/09/18/adventures-in-galaxy-output-collections/
>>>
>>> On 20 October 2015 at 08:48, Steve Cassidy <steve.cass...@mq.edu.au>
>>> wrote:
>>>
>>>> Hi all,
>>>>   I'm trying to understand how to write a tool that generates a dataset
>>>> rather than a single output file.  I've tried following all of the examples
>>>> but I'm stuck, so I thought I would distil down the simplest example I
>>>> could write and ask for help here.
>>>>
>>>> So here's my example:
>>>>
>>>> https://gist.github.com/stevecassidy/0fa45ad5853faacb5f55
>>>>
>>>> it's a simple python script that writes three files to a directory
>>>> named for the single input parameter.
>>>>
>>>> I think one of the problems I'm having is knowing where to write the
>>>> output to. I've run this under planemo serve and the job runs, creating the
>>>> output directory within the 'job_working_directory/000/1/SampleDataset'
>>>> directory, however my dataset doesn't contain anything so clearly my
>>>> outputs directive isn't working:
>>>>
>>>>     <outputs>
>>>>         <collection type="list" label="$job_name" name="output1">
>>>>             <discover_datasets pattern="__name_and_ext__"
>>>> directory="$job_name" />
>>>>         </collection>
>>>>     </outputs>
>>>>
>>>> ($job_name is the name of the directory that is being written to,
>>>> SampleDataset in this case)
>>>>
>>>> Any help in getting this example working would be appreciated.
>>>>
>>>> Thanks,
>>>>
>>>> Steve
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Department of Computing, Macquarie University
>>>> http://web.science.mq.edu.au/~cassidy/
>>>>
>>>> ___________________________________________________________
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>>>>
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>>
>>
>>
>>
>> --
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy/
>>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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>



-- 
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/
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