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.

Best,
J.

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
> http://localhost:8080/api/tools/tophat?key=....
> returns
> {
>    "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
> conditional.
> 
> Is there currently a way to specify (or see) these missing fields?
> 
> Thanks,
> Clare
> 
> 
> -- 
> 
> 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
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