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-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:
<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
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