Le 18 janv. 2018 à 12:34, Peter Cock <p.j.a.cock@googlemail.com> a écrit :

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/e2fa1c599b6670b418479447fe5a181a97a6c834/.travis.yml#L126

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-data
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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