Ah, thankyou, yes, I can now get results by using patterns to match the output. I used your example but prepend 'simple' to the filename and then searches for that with:
<discover_datasets pattern="simple(?P<name>.*)" /> this solves the problem for the sample script but not generally since in general I can't predict the filenames that will be generated - this is a tool for downloading data from a repository which could be text, audio or video data. If I don't use the 'simple' prefix and omit the file extension I still get my data but I also get three other files which are temporary scripts generated by galaxy and placed in the working directory. So, back to trying to put things in a subdirectory. It turns out that the issue I was having was as you pointed out earlier, the directory attribute to discover_datasets doesn't allow variables, so I need to write to a fixed directory name: <discover_datasets pattern="(?P<name>.*)" directory="SampleDataset" /> This now works! I had thought that I'd need to use a unique directory name but since galaxy runs each job in a separate directory, this isn't required. My real tool now works too after following the same pattern. Thanks for your help. I'll see if I can write this up in a blog post. Steve On 21 October 2015 at 00:06, Peter van Heusden <p...@sanbi.ac.za> wrote: > I poked around at your tool XML and the code a bit and the problem is > directory="$job_name". Galaxy expects to collect files from the job's > working directory - basically the current working directory the job runs > in. The directory= argument doesn't have variables expanded as far as I can > tell. In any event it is used in walk_over_extra_files() that is in > lib/galaxy/tools/parameters/output_collect.py - if you look there you see > that it is simply appended to the job's working directory. > > So if you use: > > <discover_datasets pattern="(?P<name>.*)\.txt" /> > > (note the < and > - this is effectively the regexp > r"(?P<name>.*)\.txt" with the < and > escaped out) > > And alter the code so that it just writes files to the current directory, > then you'll pick up the files one.txt, two,txt and three.txt. > > Peter > > On 20 October 2015 at 12:28, Steve Cassidy <steve.cass...@mq.edu.au> > wrote: > >> Sorry, it was just an example of a tool that works - the file that it >> writes out is put into that directory, so I assume that's where my files >> should end up too. >> >> Steve >> >> On 20 October 2015 at 21:12, Peter van Heusden <p...@sanbi.ac.za> wrote: >> >>> Sorry, I don't understand - what does the Upload File tool have to do >>> with this? >>> >>> On 20 October 2015 at 11:49, Steve Cassidy <steve.cass...@mq.edu.au> >>> wrote: >>> >>>> 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/ >>>>>>>> >>>>>>>> ___________________________________________________________ >>>>>>>> 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/ >>>>>> >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> 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/ >>>> >>> >>> >> >> >> -- >> 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/ > -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/
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