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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