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'"

-----------------------
Questions:

Q: How can I use this string with Cheetah, or is the low-level Python object 
(i.e. a list) also available (that is used to generate this string)?

Q: You can use a <filter> for the <output> parameters, which doesn't work with 
$report_options in this case, so how to use the <filter> with 
'multiple_select="True"'?

Q: While trying out some Cheetah functionality (as explained in the Cheetah 
manual), I've came across a number of 'things' in the Cheetah documentation 
that aren't supported in Galaxy tool XML files. Is there some documentation 
available showing what is possible and what isn't?

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.
-----------------------


Any help or pointers / examples are greatly appreciated!

Some links:
- Cheetah Manual: 
http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html
_ Excellent post about Cheetah on the mailing list: 
http://gmod.827538.n3.nabble.com/Bitten-by-a-Cheetah-long-td2760688.html

Regards,

Marcel
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