Dear Dannon,

Thank you for your answer, it works better now that I know the steps ID for my workflow.

I have another question though.

The second step of my WF uses a parameter input named "prefix". I really need to specify it when I launch the WF using the API.

When i display the WF using the url you gave me, the parameters prefix, is not there and when I use this in my command line, the specified Value is not read by Galaxy.

python workflow_execute_parameters.py 43359c833b8977b01d6237d9b839dc27 http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e985db '10=hda=52ea4fd71e9f7c3f' 'param=export_sbw=prefix=test'

Could you help me on that ? How do I give a value to a parameter if it does not appear in the WF description ??

Thanks in advance, -- Olivia

Le 23/04/14 18:40, Dannon Baker a écrit :

Hi Olivia!

It's probably talking about the "workflowstep" object with identifier 8. If you request the description of this workflow via the API (http://yourgalaxyinstance.org/api/workflows/<the id of this workflow>"), you'll be given the exact step identifiers to use. In other words, unless this is the first workflow ever created on a brand new galaxy instance, your step ids will not be 0 and 1.

-Dannon

On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual <olivia.doppelt@pasteur.fr mailto:olivia.doppelt@pasteur.fr> wrote:

Dear developpers,

I'm trying to launch a small workflow using the api script
workflow_execute_parameters.py

I have 2 steps: the input data step and a second step which needs
a parameter called prefix.


The workflow is attached to this email.

I get an error on the parameters inputs which asks me to specify
information about an 8th step (which does not exist)


Is there a test case available to use this script ?

Please keep me informed on that.

Have a nice day,

-- 
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur


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Dear Dannon,

when the parameter (that I need to fix) is 'set at runtime', the value that it gets is: __lt__galaxy.tools.parameters.basic.RuntimeValue

---- python workflow_execute_parameters.py 43359c833b8977b01d6237d9b839dc27 http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e985db '14=hda=52ea4fd71e9f7c3f' 'param=export_sbw=prefix="test"'

---- the parameter prefix needs to be set at the value "test" (I tried without the quotes also)

---

Here is what you asked for:

{ "id": "f2db41e1fa331b3e", "inputs": { "14": { "label": "input Dataset", "value": "" } }, "model_class": "StoredWorkflow", "name": "export_WF", "published": false, "steps": { "14": { "id": 14, "input_steps": {}, "tool_id": null, "type": "data_input" }, "15": { "id": 15, "input_steps": { "inputs_0|input": { "source_step": 14, "step_output": "output" } }, "tool_id": "export_sbw", "type": "tool" } }, "tags": [], "url": "/api/workflows/f2db41e1fa331b3e" }

----

as you can see, the parameter called prefix, is not there.

Thank you for your help

-- Olivia

Le 25/04/14 19:49, Dannon Baker a écrit :

Olivia,

Is the parameter set to 'set at runtime' when you view the workflow in the editor? Could you send me the workflow json (just the http://127.0.0.1:8080/api/workflows/<workflow_id>/ bit)?

-Dannon

On Fri, Apr 25, 2014 at 5:26 AM, Olivia Doppelt-Azeroual <olivia.doppelt@pasteur.fr mailto:olivia.doppelt@pasteur.fr> wrote:

Dear Dannon,

Thank you for your answer, it works better now that I know the
steps ID for my workflow.

I have another question though.

The second step of my WF uses a parameter input named "prefix". I
really need to specify it when I launch the WF using the API.

When i display the WF using the url you gave me, the parameters
prefix, is not there and when I use this in my command line, the
specified Value is not read by Galaxy.

python workflow_execute_parameters.py
43359c833b8977b01d6237d9b839dc27
http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e
a799d38679e985db '10=hda=52ea4fd71e9f7c3f'
'param=export_sbw=prefix=test'

Could you help me on that ? How do I give a value to a parameter
if it does not appear in the WF description ??

Thanks in advance,
--
Olivia


Le 23/04/14 18:40, Dannon Baker a écrit :

...

Hi Olivia!

It's probably talking about the "workflowstep" object with
identifier 8.  If you request the description of this workflow
via the API (http://yourgalaxyinstance.org/api/workflows/<the id
of this workflow>"), you'll be given the exact step identifiers
to use.  In other words, unless this is the first workflow ever
created on a brand new galaxy instance, your step ids will not be
0 and 1.

-Dannon


On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual
<olivia.doppelt@pasteur.fr <mailto:olivia.doppelt@pasteur.fr>> wrote:

    Dear developpers,

    I'm trying to launch a small workflow using the api script
    workflow_execute_parameters.py

    I have 2 steps: the input data step and a second step which
    needs a parameter called prefix.


    The workflow is attached to this email.

    I get an error on the parameters inputs which asks me to
    specify information about an 8th step (which does not exist)


    Is there a test case available to use this script ?

    Please keep me informed on that.

    Have a nice day,

    -- 
    Olivia Doppelt-Azeroual, PhD
    Tel: 92 15
    CIB - Institut Pasteur


    ___________________________________________________________
    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/

    To search Galaxy mailing lists use the unified search at:
    http://galaxyproject.org/search/mailinglists/

-- 
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur