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-based-on-variables-td4141375.html.
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/