No legal value defined in a planemo test for param type="select" and options="from_file"
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<mailto: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
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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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<mailto: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<mailto: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 ___________________________________________________________ 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/
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
___________________________________________________________ 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/
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 olivier.inizan@inra.fr<mailto: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 18 janv. 2018 à 12:34, Peter Cock <p.j.a.cock@googlemail.com<mailto: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/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 ___________________________________________________________ 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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