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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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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
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/>
java -cp /Splitter1.jar /Common.jar
SplitterModule $input $output1 $output1.id
$__new_file_path__
<inputs>
<param format="txt" name="input" type="data" label="reads">
</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/>
java -cp Integrator1.jar:Common.jar
IntegratorModule $input $output
<inputs>
<param format="interval" name="input" type="data" label="pp">
</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
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
DISCLAIMER
==========
This e-mail may contain privileged and confidential information which
is the property of Persistent Systems Ltd. It is intended only for the
use of the individual or entity to which it is addressed. If you are
not the intended recipient, you are not authorized to read, retain,
copy, print, distribute or use this message. If you have received this
communication in error, please notify the sender and delete all copies
of this message. Persistent Systems Ltd. does not accept any liability
for virus infected mails.
