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.gruening@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&am...
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