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 > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/