Hi Tiago,

in the following my few comments. If you like to submit this to
IUC-tools a WIP would be nicer to comment on.


* Booleans can be treated like this.

 <param name="search_complete_random_tree" type="boolean"
checked="False" truevalue="--search_complete_random_tree" falsevalue=""
display="checkboxes" label="Start ML optimization from a complete random
starting tree (-d)" />

Note the changed truevalue and falsevalue. This will reduce this:

#if str ($selExtraOpts.search_complete_random_tree) == "true":
--search_complete_random_tree
#end if

to

$selExtraOpts.search_complete_random_tree

because $selExtraOpts.search_complete_random_tree evaluates now to
--search_complete_random_tree if it is checked, otherwise its empty.

* sys.stderr.write() ... can be removed.

* <param type="data" format="fasta" name="infile" label="Source file"/>
Can be changed to
<param type="data" format="fasta,phylip" name="infile" label="Source
file"/> to allow both filetypes and to make the UI simpler.

*  <param name="base_model" type="select" label="Substitution Model
(-m)"> -> put the (-m) please in help="" not in the label

Thanks!
Bjoern




Am 02.11.2015 um 22:29 schrieb Tiago Antao:
> Hi,
> 
> 
> On Tue, 20 Oct 2015 14:48:08 +0200
> Bjoern Gruening <bjoern.gruen...@gmail.com> wrote:
> 
>> What kind of dependencies do you have? Python/Perl?
>> Consider contributing to tools-iuc 
>> (https://github.com/galaxyproject/tools-iuc). We can probably help
>> you and guide you your way.
> 
> 
> Before I start working on RAD-Seq, I had a "warm-up exercise" with
> RAxML.
> I have upgraded Alex's version of the RAxML tool (with his knowledge -
> I am also Ccing him) to a more recent version. I also added one meager
> test to start with.
> 
> You can find this on
> https://testtoolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&operation=view_or_manage_repository&id=fd4191b7bdcd01d2
> 
> Or, if you prefer github:
> https://github.com/tiagoantao/galaxy_tools/tree/master/tools/raxml
> 
> I am willing to maintain this tool (and associated package). This can
> be transferred to tools-iuc as soon as people are happy with the result.
> 
> After this is finalized, I will have a look at the RAD-Seq work.
> 
> Tiago
> 
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