Dear all,

We've been actively developping xml wrappers for new programs in our instance of Galaxy and we encountered some problems with multiple outputs number while using these tools in a workflow.

1/ In the first case, inputs can be 1 single file or 2 paired files and the program output name is different depending on which case. The input problem is resolved using <conditional> and following we implemented the outputs as such:

<data name="nameSorted.single.bam" format="bam" from_work_dir="alignReads/alignReads.nameSorted.bam" label="nameSorted single" >
            <filter>inputs['paired_or_single'] == 'single'</filter>
<data name="nameSorted.paired.bam" format="bam" from_work_dir="alignReads/alignReads.nameSorted.PropMapPairsForRSEM.bam" label="nameSorted paired" >
            <filter>inputs['paired_or_single'] == 'paired'</filter>

However, when using this tool in a workflow, the toolbox always presents the 2 outputs, whether we choose 1 or 2 inputs. Is there any way to have only one output in the toolbox but from a different file depending on the input ?

2/ the second case is very similar to the one described in When we input a single file the output is also a single file, and when we input two paired files the program outputs two files. Thanks again to the <conditional> tag the input problem was taken care of, but we would like the workflow toolbox to present 1 or 2 outputs (ideally with all 3 names different) depending on how many files are in the input. Is there any way to do so other than making 2 different versions of the xml or displaying all 3 outputs in the workflow toolbox ?

Thanks in advance,


Pierre Pericard
IE CDD - Projet Peptisan
Service Informatique et Bio-informatique (SIB)
Station Biologique - CNRS-UPMC
Place Georges Teissier, 29680 Roscoff

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