Hello,

I'm trying to write my own wrappers for Cufflinks,Cuffcompare,Cuffdiff, 
learning mostly by looking at the existing tools.
I have a question regarding the multiple input/output implementation in 
CuffCompare:

In CuffCompare, the XML can accept multiple input files (with a <repeat>), and 
the <output> section contains the following statements (labels removed for 
brevity):
=========
 <outputs>
        <data format="txt" name="transcripts_accuracy" label="" 
from_work_dir="cc_output" />
        <data format="tabular" name="input1_tmap" label="" 
from_work_dir="input1.tmap" />
        <data format="tabular" name="input1_refmap" label="" 
from_work_dir="input1.refmap"/>

        <data format="tabular" name="input2_tmap" label="" 
from_work_dir="input2.tmap">
            <filter>len( input_files ) > 0</filter>
        </data>
        <data format="tabular" name="input2_refmap" label="" 
from_work_dir="input2.refmap">
            <filter>len( input_files ) > 0</filter>
        </data>
        <data format="tabular" name="transcripts_tracking" label="">
            <filter>len( input_files ) > 0</filter>
        </data>

        <data format="gtf" name="transcripts_combined" label="" 
from_work_dir="cc_output.combined.gtf"/>
    </outputs>
======

Assuming cuffcompare generates a TMAP and REFMAP file for each input file, does 
this mean the wrapper tool retrieves only the first and second input files' 
TMAP and REFMAP files ? and others are ignored ? Or is there some galaxy black 
magic python code that iterates multiple inputs and imports them all ?

Thanks,
 -gordon

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