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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