Thanks for the info!
I am confused though because the code in tools.py was what was making
me think I could run a tool with specified inputs. ie I was looking at
def create( ... )
# Set up inputs.
inputs = payload[ 'inputs' ]
params = util.Params( inputs, sanitize = False )
template, vars = tool.handle_input( trans, params.__dict__ )
I think that handle_input() executes the tool? Also, separately there
is a method called _run_tool() (although unlike _rerun_tool() I can't
see anything that calls it).
So, I thought from looking at the surface, that the tool-running code
was there and that I just didn't know what data structure to pass into
payload['inputs'] . Is it not doing what I think?
On 23 August 2012 23:00, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
> Unfortunately, the tools API isn't at all complete right now. The tools API
> was driven by Trackster/Sweepster needs, so rerunning tools works well but
> running tools from scratch doesn't.
> Practically, this means that the things you want to do, e.g.
> *view tool parameters;
> *set tool input datasets;
> are not yet supported.
> As always, community contributions are welcome and encouraged.
> On Aug 23, 2012, at 4:10 AM, Clare Sloggett wrote:
>> Hi guys,
>> The Tools API is currently working for me from galaxy-central, but I'm
>> not sure how to correctly run a tool. Are there any example scripts,
>> as there are for some other parts of the API? Specifically I want to
>> find out what the expected payload fields are when I post to CREATE to
>> run a tool.
>> Some of the fields are clear to me just from the api/tools.py code
>> (e.g. 'tool_id') but others are not (e.g. how the input datasets and
>> parameters are specified).
>> A separate question:
>> How do we specify "Advanced" or conditional-dependent fields for a
>> tool? Some of these fields are necessary to run the tool at all.
>> For instance, on my system, calling
>> "description": "Find splice junctions using RNA-seq data",
>> "id": "tophat",
>> "inputs": [
>> "html": "%3Cselect%20name%3D%22input1%22%3E%0A%3C/select%3E",
>> "label": "RNA-Seq FASTQ file",
>> "name": "input1",
>> "type": "data"
>> "label": "Conditional (refGenomeSource)",
>> "name": "refGenomeSource"
>> "label": "Conditional (singlePaired)",
>> "name": "singlePaired"
>> "name": "Tophat for Illumina",
>> "version": "1.5.0"
>> This is obviously only some of the inputs you see in the UI. I think
>> that all the Advanced fields are missing, and more importantly, any
>> input which is dependent on a conditional is missing. So the
>> refGenomeSource conditional is there, but the actual reference genome
>> field is not. The type of the reference genome field also presumably
>> depends on which value is supplied for the referenceGenomeSource
>> Is there currently a way to specify (or see) these missing fields?
>> Clare Sloggett
>> Research Fellow / Bioinformatician
>> Life Sciences Computation Centre
>> Victorian Life Sciences Computation Initiative
>> University of Melbourne, Parkville Campus
>> 187 Grattan Street, Carlton, Melbourne
>> Victoria 3010, Australia
>> Ph: 03 903 53357 M: 0414 854 759
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854 759
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: