Hi John,

I've just tried a workflow using my MIRA4 de novo wrapper:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

To keep it simple, in this example I just had two input FASTQ
files, the forward and reverse files for paired end MiSeq data.

This seemed to work fine for re-running the workflow :)

However, on loading the workflow to edit it, only the first
input file was drawn linked to the MIRA4 tool. On making
some minor workflow changes (renaming some output),
and trying to run it, the second input file seemed not to
be used.

Is this something you are aware of?

The good news is that I could "re-draw" the missing
connection from the second FASTQ file in the workflow
editor, and that appears to be working...

Peter

--

This was using the current stable release,

$ hg branch
default

$ hg heads
changeset:   10421:a477486bf18e
branch:      stable
tag:         tip
user:        Nate Coraor <n...@bx.psu.edu>
date:        Thu Sep 26 11:02:58 2013 -0400
summary:     Bugfix for tool-to-destination mapping, tool ids are
lowercased but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
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