Re: [galaxy-dev] Using the tools API
Hi Jeremy, OK, that makes sense. Thanks again! Clare On 24 August 2012 02:17, Jeremy Goecks jeremy.goe...@emory.edu wrote: I think that handle_input() executes the tool? That's the intention and it should work but it hasn't been tested. Also, separately there is a method called _run_tool() (although unlike _rerun_tool() I can't see anything that calls it). Looks like _run_tool is almost a copy of what's in create(). This is probably legacy code from refactoring that hasn't been cleaned up yet. 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? I think your inference is correct, but, yes, there's the problem of specifying the tool input data structure. Tool inputs are specified as dictionaries (often with nested dictionaries for things like conditionals), so you could construct an appropriate input dictionary and could (likely) run a tool. However, there's no help in the API right now to help you construct an appropriate dictionary for a tool; this is the big missing piece in the tools API. Best, J. -- 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Using the tools API
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
___
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:
http://lists.bx.psu.edu/
___
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:
http://lists.bx.psu.edu/
Re: [galaxy-dev] Using the tools API
Hi Jeremy,
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?
Thanks,
Clare
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.
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
___
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:
http://lists.bx.psu.edu/
--
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:
http://lists.bx.psu.edu/
Re: [galaxy-dev] Using the tools API
I think that handle_input() executes the tool? That's the intention and it should work but it hasn't been tested. Also, separately there is a method called _run_tool() (although unlike _rerun_tool() I can't see anything that calls it). Looks like _run_tool is almost a copy of what's in create(). This is probably legacy code from refactoring that hasn't been cleaned up yet. 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? I think your inference is correct, but, yes, there's the problem of specifying the tool input data structure. Tool inputs are specified as dictionaries (often with nested dictionaries for things like conditionals), so you could construct an appropriate input dictionary and could (likely) run a tool. However, there's no help in the API right now to help you construct an appropriate dictionary for a tool; this is the big missing piece in the tools API. Best, J. ___ 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: http://lists.bx.psu.edu/
