I am trying to figure out how to get static files stored on my Linux machine to go with all of the tool information and database files to my Windows box via Pulsar. Right now I do this by creating a select parameter with options tag with from_ file pointing to file but the parameter is unused. Is there a better way to specify files to be brought into the job working directory or specify a batch of files that go wherever the tool is sent via pulsar.
There is not currently a way to do this. This is a serious deficiency in the way Pulsar operations. The work around is to make the script executable directly and place it on Pulsar's PATH manually - so the tool XML will not have an interpreter tag for instance. I hope that with the April release of Galaxy (16.04) that I will finally get around to introducing a way to annotate files needed by the tool wrapper in the tool XML itself - this will allow Galaxy to know what to transfer to Pulsar (https://github.com/galaxyproject/galaxy/issues/1609).