No legal value defined in a planemo test for param type="select" and options="from_file"

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No legal value defined in a planemo test for param type="select" and options="from_file"

Olivier Inizan-2
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
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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Re: No legal value defined in a planemo test for param type="select" and options="from_file"

Peter Cock
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 <[hidden email]> 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
> [hidden email]
> Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
> Plateforme bioinformatique Migale
> Bâtiment 233
> Domaine de Vilvert
> 78352 Jouy-en-Josas
>
>
> ___________________________________________________________
> 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/
___________________________________________________________
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:
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Re: No legal value defined in a planemo test for param type="select" and options="from_file"

Olivier Inizan-2
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
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 <[hidden email]> 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 <[hidden email]> 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
[hidden email]
Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
Plateforme bioinformatique Migale
Bâtiment 233
Domaine de Vilvert
78352 Jouy-en-Josas


___________________________________________________________
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/


___________________________________________________________
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/
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Re: No legal value defined in a planemo test for param type="select" and options="from_file"

Peter Cock
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 <[hidden email]> 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
> [hidden email]
> 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 <[hidden email]> 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 <[hidden email]>
> 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
> [hidden email]
> Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
> Plateforme bioinformatique Migale
> Bâtiment 233
> Domaine de Vilvert
> 78352 Jouy-en-Josas
>
>
> ___________________________________________________________
> 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/
>
>
___________________________________________________________
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/
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Re: No legal value defined in a planemo test for param type="select" and options="from_file"

Olivier Inizan-2
Thank you Peter :)
I could also change the code in the wrapper and use an <options=from_data_table> 
The documentation states that this approach is more generic (The mechanism from_file is discouraged …)

Thanks again.
Olivier 

Olivier INIZAN
Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
Plateforme bioinformatique Migale
Bâtiment 233
Domaine de Vilvert
78352 Jouy-en-Josas

Le 18 janv. 2018 à 12:34, Peter Cock <[hidden email]> 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 <[hidden email]> 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
[hidden email]
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 <[hidden email]> 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 <[hidden email]>
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
[hidden email]
Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
Plateforme bioinformatique Migale
Bâtiment 233
Domaine de Vilvert
78352 Jouy-en-Josas


___________________________________________________________
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/




___________________________________________________________
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/