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.SteveOn 20 October 2015 at 21:12, Peter van Heusden <pvh@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.cassidy@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.SteveOn 20 October 2015 at 19:57, Peter van Heusden <pvh@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?PeterOn 20 October 2015 at 09:52, Steve Cassidy <steve.cassidy@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.SteveOn 20 October 2015 at 18:33, Peter van Heusden <pvh@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).On 20 October 2015 at 08:48, Steve Cassidy <steve.cassidy@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: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
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