Perfect. Thanks a lot. Maybe one could add a note to planemo --help that
command specific help can be obtained with planemo command --help.
Best,
Matthias
On 12.07.2017 16:57, Peter Cock wrote:
Try:
planemo lint --fail_level error sleepwaste.xml
The default is to fail if there are warnings.
Peter
On Wed, Jul 12, 2017 at 3:55 PM, Matthias Bernt <m.be...@ufz.de> wrote:
Hi Peter,
I just call planemo l sleepwaste.xml
Best,
Matthias
On 12.07.2017 16:54, Peter Cock wrote:
How are you running planemo lint - in particular is it set
to fail if there are any warnings present (like your missing
citation warning)?
Peter
On Wed, Jul 12, 2017 at 3:52 PM, Matthias Bernt <m.be...@ufz.de> wrote:
Dear list,
In order to test the job resubmission feature I wrote a little tool for
galaxy that just wastes a specified (minimum) time and memory (using
different programming languages) for testing the new DRMAA job runner
that I
wrote.
When linting it with planemo seemingly all tests are successful, but in
the
end I still get a fail -- verbose mode is also of no help here.
Applying linter tests... CHECK
.. CHECK: 7 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 3 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.0].
.. CHECK: Tool defines a name [Waste time and memory].
.. CHECK: Tool defines an id [sleepwaste].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: No citations found, consider adding citations to your tool.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Failed linting
The test of the tool are all successful. Any ideas what is wrong?
Once the problems are solved, would such a tool also be useful in the
toolshed?
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
Please keep all replies on the list by using "reply all"
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--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
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/
