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.js

but I haven't used it myself. Hope this helps,
Brad