Erik and Jeremy;
I am a JBrowse Dev hoping to add the ability to export data directly from JBrowse (JavaScript) to Galaxy
The API could be used for this.
Specifically, you could do an upload for the user from a URL via the tools API. I know that Brad Chapman (cc'd) has done this successfully recently. Brad, can you share the parameters used to do this?
Definitely, you want to do a POST to: /api/tools?key=YOURAPIKEY with a JSON payload of: {"tool_id": "upload1", "history_id": "identifier of history to use", "params": {"file_type": "vcf", "dbkey": "hg19", "files_0|url_paste": http://jbrowse-server.org/path/to/file.vcf", "files_0|NAME": "file_name_for_history.vcf"}} This is all new since the last galaxy-dist release, so you'd need a recent galaxy-central server. Passing it back to Jeremy, there is also a Javascript wrapper around the tools API which might help: https://bitbucket.org/galaxy/galaxy-central/src/tip/static/scripts/mvc/tools... but I haven't used it myself. Hope this helps, Brad