You can still use the workaround on TravisCI by creating a Galaxy instance and telling planemo to use it (rather than the default of letting planemo create the test Galaxy instance).
I do this here for example:
https://github.com/peterjc/pico_galaxy/blob/e2fa1c599b6670b418479447fe5a181a...
Peter
On Thu, Jan 18, 2018 at 11:21 AM, Olivier Inizan olivier.inizan@inra.fr wrote:
Thank you Peter !
If I have well understood the workaround implies having a local galaxy instance with the .loc file. But for a planemo test with Travis CI I still will have the error. Is it correct ?
Thanks again Peter.
Olivier
Olivier INIZAN olivier.inizan@inra.fr Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement Plateforme bioinformatique Migale Bâtiment 233 Domaine de Vilvert 78352 Jouy-en-Josas
Le 17 janv. 2018 à 17:39, Peter Cock p.j.a.cock@googlemail.com a écrit :
It sounds like it could be this issue?:
https://github.com/galaxyproject/planemo/issues/530
If so, the good news is there is a workaround (see issue discussion).
Peter
On Wed, Jan 17, 2018 at 4:24 PM, Olivier Inizan olivier.inizan@inra.fr wrote:
Dear list,
I am trying to write a test with a param type "select" and options "from_file". I have the following param section in the wrapper:
<!-- Database Choice -->
<param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> <options from_file="frogs_db.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param>
And I wrote the following test section:
<test> ... <param name="ref_file" value="db.fasta"/> </test>
The planemo test command failed with the following message: RunToolException: Error creating a job for these tool inputs - Parameter ref_file requires a value, but has no legal values defined.
Looking at the planemo documentation I saw the entry "test index (.loc) data": http://planemo.readthedocs.io/en/latest/writing_how_do_i.html#test-index-loc... but it seems to work with <options from_data_table>.
Have you any test example working with <options from_file> ?
Thanks for your help.
Olivier
Olivier INIZAN olivier.inizan@inra.fr Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement Plateforme bioinformatique Migale Bâtiment 233 Domaine de Vilvert 78352 Jouy-en-Josas
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