Thanks for the pointer to the updated wrapper and the optional tag.

So is the behavior of the optional="true" tag that if the field form is
left empty for that parameter then it will not be passed to the tool?
I am wondering if a more sophisticated behavior on the UI side of things
for the "optional" tag would still allow for recording that the parameter
is using the default value for the version of that tool but not actually
pass that parameter on the command line in case it influences the behavior
of the tool? Thinking of parameters that should have a default value but
whose actual presence on the command line changes what happens. Though, I
guess this could be done by simply deleting the default value in the
optional parameter has one?

Maybe if the optional tag enabled the parameter itself to be toggled on/off
(grayed out/regular text)? This way a block of advanced parameters could be
enabled without requiring that they all be passed to the tool (or deleting
all their values if they are marked optional).

Just a small note, the update to the tophat wrapper was to the maximum
number of alignments instead of mismatches.

Thanks again,

On Fri, Feb 10, 2012 at 11:28 AM, Peter Cock <>wrote:

> On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks <>
> wrote:
> >> On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren <>
> wrote:
> >>> Hello,
> >>>
> >>> I was recently adjusting advanced parameters when running Tophat in
> Galaxy
> >>> and noticed that when advanced parameters are used, every field is
> converted
> >>> and submitted as command line parameter to the tool at runtime. Without
> >>> changing any of the default values I get a different tophat result
> than if
> >>> advanced parameters are left off.
> >>
> >> That sounds like a bug in the wrapper.
> >
> > Recent Tophat versions have changed parameters and default values
> > again. I made the following changes in 3bd8bed55631 to make the
> > wrapper compatible with Tophat 1.4.0:
> >
> > *removed junctions_filter parameter
> > *changed the default value for max-mismatches from 40 to 20
> >
> > This should ensure that enabling advanced parameters but leaving
> > them untouched yields the same results as using default parameters.
> >
> > J.
> Wouldn't it be better not to have the default value 40 (or 20) in the
> wrapper
> at all? i.e. Leave it out, so that by default that argument isn't used, so
> that
> tophat uses the default it wants to use.
> Peter
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