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 http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files we implemented the outputs as such: <outputs> <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> <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> </data> </outputs> 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 http://dev.list.galaxyproject.org/outputting-different-numbers-of-files-base.... 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 -- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique - CNRS-UPMC Place Georges Teissier, 29680 Roscoff FRANCE http://abims.sb-roscoff.fr/