We are also feeling the hurt of not being able to carry the input
dataset names through a complex workflow. We are also very interested
in a solution similar to what Dave Walton has proposed,. Dave, would it
be possible to receive a copy of your modified code? Does it work when
there are
on_string seems to be defined for datatool parameters only.
There's a common idiom for looking up fields from the relevant .loc
files for things like all_fasta - it's not pretty but it does work -
eg from the bowtie wrapper:
--ref=${ filter( lambda x: str( x[0] ) == str(
$refGenomeSource.index
This is a big part of the reason we did this.
I will push it out for the galaxy team to look at. If for some reason the
don't approve it I can share our change directly with you.
Dave
On Sep 1, 2011, at 6:39 PM, Ross ross.laza...@gmail.com wrote:
FWIW: This sounds like a useful idea to me.
It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within the
parameter to be an English sentence that would become the label for the
output. I.e.,
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.
This is a common idiom -
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes
based on whether or not you've checked a checkbox (or a way to change the
label of the output based on whether or not the checkbox was checked). So
my idea below did work, but it seems like a hack. Which is why I
Most times I need a user supplied label substring. I'm not sure how
else to conditionally set a string to a predetermined value other than
with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now
deprecated) post job exec hook to
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the
output name BEFORE execution... although that doesn't make sense. In any
case, I couldn't get it to work. Also, in the example below the % should
really be # right? Anything anyone can think of that I might be
you can use label=${input.name}
Shaun
Quoting Nikhil Joshi najo...@ucdavis.edu on Thu, 25 Aug 2011 03:10:21 -0700:
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the
output name BEFORE execution... although that doesn't make sense. In any
case, I
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25,
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to be
true.
- Nik.
___
Please
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
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