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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