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.bernt(a)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.bernt(a)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.bernt(a)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
>> -------------------------------------------
>>
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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.bernt(a)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
-------------------------------------------