Hi Craig,

Thanks for your interest in the galaxy API.  For the parameters you're 
uncertain about:

The 'workflow_id' is indeed the encoded workflow id.  You can get this by 
encoding it yourself, or doing a GET on /api/workflows for a list of *all* 
workflows and their encoded id's (see example below)
The 'history' is either a name for a new history to be created, or a string of 
the format "hist_id=<encoded history_id to use>", if you have an existing 
history that you'd like the results to appear in.
And the last parameter is a three part string.  The first part is the step that 
the input should be mapped to, the second part is the *type* of input it is, 
and the third step is the actual encoded id.  The type is going to be either 
ldda for a library dataset, or hda for a history dataset.

All of these encoded id's are discoverable through the API itself.  Try using 
scripts/api/display.py to view /api/workflows, 
/api/workflows/<encoded_workflow_id> to get a feel for what's available to you.

Lastly, an example of how the run_workflow component of the api could be used 
as a part of an external pipeline can be found in 
scripts/api/example_watch_folder.py.  This script monitors a particular folder 
for files, uploads them to galaxy, and executes a workflow on them.

Hope this helps, and definitely let me know if I can answer any more questions 
or if you have feedback about the API.

-Dannon


On Dec 1, 2011, at 7:32 PM, Craig Blackhart wrote:

> I am newish to Galaxy and trying to learn how I might integrate it with our 
> workflows and LIMS for automated data handling.  I am aware of the API and 
> have looked up all the documentation that I could find.  However, there are 
> many things I cannot make sense of, and have not been able to find 
> information to help me out.  I think a good place to start asking questions 
> is with how to run workflow_execute.py and ask what each of the parameters 
> are and where to get the information from them
>  
> Arguments
>                *API key – got this and understand
>                *url – got this and understand
>                *workflow_id – I have created workflows and have been able to 
> find what looks to be a workflow_id by clicking on the workflow name and 
> selecting “Download or Export”.  It seems this may be correct, is it?
>                *history – a named history to use?  Should this already exist? 
>  I have no idea here.
>                *step=src=dataset_id - ??? I have no idea ???  I have seen how 
> to create data libraries manually at the command line; does this factor in?
>  
> If anyone has information they can help me out with, it would be much 
> appreciated.
>  
> Thanks
>  
> Craig Blackhart
> Computer Scientist
> Applied Engineering Technologies
> Los Alamos National Laboratory
> 505-665-6588
> This message contains no information that requires ADC review
>  
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