Question: Bioblend - Passing a non-datasets parameter in toolClient.run_tool ?
gravatar for lindfors.erno
4.1 years ago by
lindfors.erno30 wrote:

Hi all,

I am trying to pass a non-dataset parameter in toolClient.run_tool.

More specifically, I am running the following code.
from bioblend.galaxy import GalaxyInstance
from bioblend.galaxy.histories import HistoryClient
from import ToolClient
from bioblend.galaxy.datasets import DatasetClient
galaxyInstance = GalaxyInstance(url=GALAXY_URL, key=API_KEY)
historyClient = HistoryClient(galaxyInstance)
toolClient = ToolClient(galaxyInstance)
datasetClient = DatasetClient(galaxyInstance)
history = historyClient.create_history('tmp')
testFile = toolClient.upload_file(PATH_NAME, history['id'], type='txt')
params = {'param': 'cond.choice', 'value': 'yes','cond.test_file':{'src': 'hda', 'id': testFile['outputs'][0]['id']}}
output = toolClient.run_tool(history_id=history['id'], tool_id=TOOL_ID, tool_inputs=params)

I am using the following xml file in Galaxy server:
<tool id="CondTest_R" name="CondTest" version="1.1.0">
  <description>Makes a conditional test</description>
  <command interpreter="Rscript">CondTest.R $out_file1 ${cond.choice} ${cond.te$
    <conditional name="cond">
      <param name="choice" type="select" label="Do you want to read numbers fro$
        <option value="no">no</option>
        <option value="yes">yes</option>
      <when value="no">
        <param name="test_file" type="hidden" value="NULL"/>
      <when value="yes">
        <param name="test_file" type="data" format="txt" label="Test file"/>

This does not work properly - I see from Galaxy server log that 'cond.choice' gets 'no' but I assign 'yes' to it in params = {...}.

I am pretty sure I am doing the parameters setting incorrectly in params = {...} since I have tested this tool works properly when I run it directly from Galaxy server's web interface.

Does anyone have an idea what I am doing incorrectly in the parameters settings?
In other words, what is the correct way to assign a non-dataset parameter in toolClient.run_tool?

To me it seems the documentation of toolClient.run_tool in is not very informative but from the documentation of run_workflow I got a hint that it could work something like what I am using it in the code above.

Thanks in advance,
Erno Lindfors


bioblend software error galaxy • 1.6k views
ADD COMMENTlink written 4.1 years ago by lindfors.erno30
gravatar for ablumenf
3.9 years ago by
United States
ablumenf10 wrote:

*** Solved ***

I did a bit more searching and found that the solution is to use the | character instead of the . in naming the parameter in the conditional. So in the example above it would be cond|choice . 


*** Original comment ***

Hi Erno,

I came across this post while I was researching an issue I'm having and thought you might be able to help. It looks like you were having problems setting a tool parameter that is part of a conditional. I have been having a similar problem, where I can't find the right way to change certain parameters. Specifically, I am trying to set a tool parameter when running a workflow, and can only change some of the parameters in the tool. Changing a parameter outside the conditional works fine, but not inside it. In your example above, dId using the format cond.choice work, or is there a different way to reference that parameter?  My full post is here: Setting clipping sequence as workflow parameter when running FASTX Clipper from BioBlend API. Any help would be appreciated. Thanks!

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by ablumenf10

Correct - unfortunately the workflow and tool APIs work fairly differently - and the tool API requires parameters in a flat dictionary - so cond|choice would be the key to specify a parameter for the the tools API.

ADD REPLYlink written 3.9 years ago by jmchilton1.1k

Yes the cond|choice indeed solved this, more specifically the follow parameter setting works:
params = {'cond|choice': 'yes', 'cond|test_file':{'src': 'hda', 'id': testFile['outputs'][0]['id']}}

Thanks very much for the help!

ADD REPLYlink written 3.6 years ago by lindfors.erno30
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