I was actually able to solve my problem, turns out your have to execute the 
javascript in the response from the POST request. I guess if you use a simple 
html form it is automatic hence why it wasn’t stressed in the link.

> On Jan 24, 2015, at 7:56 PM, Jonathan Laperle <jonathanlape...@icloud.com> 
> wrote:
> Hi, 
> I am trying to add a custom data source to my local galaxy following 
> approximatly the methodology described here:
> https://wiki.galaxyproject.org/Admin/Internals/DataSources?action=show&redirect=Admin%2FInternals%2FData+Sources
> <https://wiki.galaxyproject.org/Admin/Internals/DataSources?action=show&redirect=Admin/Internals/Data+Sources>
> The way I went about it is :
> 1. Galaxy displays my website in the middle frame with a GET containing an 
> URL and a tool_id.
> 2. The user selects parameters and presses a button which sends a POST 
> request at the URL obtained at point 1. This request contains the URL to 
> download the file and the tool_id
> 3. Galaxy does a GET request to the given URL and downloads the file.
> For the xml file it is mostly copy-paste from the UCSC main tool except that 
> it ends with a get rather than a post.
> The communication seems to work, in fact I can see that the data is properly 
> written to a dataset_XXX.dat file at database/files/000/ just like UCSC. 
> Unfortunately, despite not detecting any error there seems to be an issue as 
> the history is never updated to reflect the fact that a file was added.
> By comparing the terminal output of UCSC main and my custom data source tool 
> I noticed that the difference was the following line which is not present 
> when I run my tool:
> - - [24/Jan/2015:19:17:30 -0400] "GET 
> /api/histories/24d84bcf64116fe7/contents HTTP/1.1" 200 - 
> " <>" "Mozilla/5.0 (Macintosh; 
> Intel Mac OS X 10_10_1) AppleWebKit/600.2.5 (KHTML, like Gecko) Version/8.0.2 
> Safari/600.2.5”
> This occurs right after:
> galaxy.jobs.handler DEBUG 2015-01-24 19:17:30,330 (110) Dispatching to local 
> runner
> The request to the history API seems to never occur with my custom tool but I 
> cannot figure out why.
> Thank you for your help.

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