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':
<galaxy.model.HistoryDatasetAssociation object at 0xb0648ac>, 'output3':
<galaxy.model.HistoryDatasetAssociation object at 0xb15170c>, 'output4':
<galaxy.model.HistoryDatasetAssociation object at 0xaf499ac>}
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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-...@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:
<tool id="sc" name="sc" version = "1.0.0" force_history_refresh="True">
<description> My tool 1 </description>
<requirements/>
<command>java -cp /Splitter1.jar /Common.jar SplitterModule
$input $output1 $output1.id $__new_file_path__</command>
<inputs>
<param format="txt" name="input" type="data" label="reads">
<label>Reads</label>
</param>
</inputs>
<outputs>
<data format="interval" name="output1" metadata_source="input"/>
</outputs>
<help>
</help>
</tool>
The following is my Integrator tool:
<tool id="gt" name="gt" version = "1.0.0">
<description> My Tool 2 </description>
<requirements/>
<command>
java -cp Integrator1.jar:Common.jar IntegratorModule
$input $output
</command>
<inputs>
<param format="interval" name="input" type="data" label="pp">
<label>File Name</label>
</param>
</inputs>
<outputs>
<data format="text" name="output"/>
</outputs>
<help>
This tool reads the reads.pp.txt file and creates smaller sized
batches of it.
</help>
</tool>
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
From: Sonali Amonkar
Sent: Tuesday, January 18, 2011 3:23 PM
To: galaxy-user@lists.bx.psu.edu
Subject: "interval" attribute for Input?
Hi,
Currently I am building a workflow which splits a file, say File 1 into chunks
of files say File1.0, File1.1, File1.2. I used the interval attribute to have
multiple outputs and got the chunks created successfully.
<data format="interval" name="output" metadata_source="input"/>
However, now I want to connect another tool to this, which Reads multiple
inputs(interval). I could not find any documentation for Input interval type.
Is this supported? If yes then where can I find the syntax?
Warm Regards,
Sonali Amonkar
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