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@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@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
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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@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@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 -------------------------------------------