Hi Peter,

Thanks very much for you answer, this was exactly the problem, I thought I was 
dealing with a Python string and the Cheetah error was not as clear as the 
Python error that you'd get when calling a function from an unsupported object.

I also joined in with one of the Breakout sessions at the Galaxy conference in 
which Dan also explained my error 

I've been toying with Cheetah a bit more now, and it's getting better real fast 
once you get the grips with it!

Thanks again, also for your nice presentation (worked very well!)

- Marcel
Van: Peter Cock [p.j.a.c...@googlemail.com]
Verzonden: donderdag 26 mei 2011 15:25
Aan: Kempenaar, M (med)
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] The powers of Cheetah, how?

On Thu, May 26, 2011 at 1:22 PM, Kempenaar, M (med)
<m.kempen...@med.umcg.nl> wrote:
> Hi list,
> I've been working on a single Galaxy tool for a while now, and I'm running
> into all sorts of difficulties that can probably all be fixed using Cheetah.
> However I've been trying several ways of utilizing the (enormous) powers of
> Cheetah but so far I'm not successful. I'll try to ask my questions as clear
> as possible, please let me know if anything is unclear.
> In my tool I use the following input parameter:
> -----------------------
>   <param name="report_options" type="select" multiple="True"
> display="checkboxes">
> <option value="overview">phyla distribution</option>
> <option value="phyladend">phyla dendograms</option>
> <option value="heatmap">heatmap</option>
> <option value="dendogram">dendogram</option>
> <option value="pca">principal component analysis</option>
> <option value="mds">multi dimensional scaling</option>
>   </param>
> -----------------------
> Each of these options corresponds to a function in my R script, thus I want
> to do an if-else if-else to execute these functions that the user selected
> (note that multiple="True").
> Now the problem is, I also use R Sweave (sweaving R output (text/graphics)
> into LaTeX) to generate a nice looking PDF report, and since that's not a
> 'real' programming/ scripting language, I can't for instance split the
> string (as I used to do in R) and check for the boxes a user selected, so my
> questions are:
> I planned on using Cheetah to include sections of Sweave LaTeX code for each
> box checked by the user, perfectly doable with an #if-#elif you'd think,
> however since the $report_options contains a comma-separated single string,
> I would need to split (or use regular expressions) to be able to do such an
> #if-#elif like:
> #if "heatmap" in $report_options.split(",")
> results in: "NotFound: cannot find 'split' while searching for 'split'"

Try changing this:

#if "heatmap" in $report_options.split(",")


#if "heatmap" in str($report_options).split(",")

Although $report_options acts a bit like a Python string, it isn't one,
and lacks lots of useful string methods. We can turn it into a string
using the Python str function.

> Q: Followup from previous question, where within the sections of my tool XML
> file can I actually use Cheetah? This of course has to do with the order in
> which a tool is executed.

I believe only within the <command>...</command> tag.

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