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/ >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > > -- > Department of Computing, Macquarie University > http://web.science.mq.edu.au/~cassidy/ >
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