Hi,
What I am trying is,
A) to write an exec_after_process for tool1(Scatterer tool). This tool1
gives multiple outputs(in the form of files names generated by Galaxy).
--
scatterer_postprocess.py
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout,
stderr):
print "Collected Dataset[Primary] is %s"%
param_dict.get('__collected_datasets__')['primary']['output1'];
Output:
Collected Dataset[Primary] is {'output2':
, 'output3':
, 'output4':
}
--
I could see these values successfully. Next,
B) I wanted to view these multiple values in the exec_prejob hook of
tool2(Gatherer)
--
gatherer_prejob.py
def exec_before_job(inp_data, out_data, param_dict, tool):
print "*** collected dataset is %s"%
param_dict.get('__collected_datasets__')['primary']['output1'];
Output:
TypeError: Error in 'Gather' hook 'exec_before_job', original message:
exec_before_job() got multiple values for keyword argument 'inp_data'
--
I am not very savy with Python for now. Can someone point me out to any
possible resolution to this issue. The reason I am writing these hooks is to
read the multiple inputs in tool2 thrown out by tool1.
Thank you for your time.
Regards,
Sonali Amonkar
From: Sonali Amonkar
Sent: Friday, January 21, 2011 8:16 PM
To: 'galaxy-dev@lists.bx.psu.edu'
Subject: "interval" attribute for Input?
Hi,
Currently I am building a workflow which splits a file into multiple chunks and
then recreates it back into one.
Following the document on
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput, I wrote
the following code.
The following is my Splitter tool:
My tool 1
java -cp /Splitter1.jar /Common.jar SplitterModule
$input $output1 $output1.id $__new_file_path__
Reads
The following is my Integrator tool:
My Tool 2
java -cp Integrator1.jar:Common.jar IntegratorModule
$input $output
File Name
This tool reads the reads.pp.txt file and creates smaller sized
batches of it.
When I try to connect and run the workflow, this is what happens:
1. The files with the names generated from the parameters are created in
the tmp folder temporarily
2. Then these are removed and converted to .dat files and placed in
database/files/000 folder with the galaxy generated numbers file names.(eg.
dataset_89.dat)
3. However, when I check the parameters in the IntegratorModule program,
I receive new dataset files generated by Galaxy and NOT the ones which were
created and should have been passed from the Splitter module
Is there a format I need to follow when writing the Integrator Module's input
parameters? Any pointer to any document which mentions this will be helpful.
Thank you for your time.
Warm Regards,
Sonali Amonkar
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