Re: [galaxy-dev] tool and planemo problems

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&gt; 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 >> ------------------------------------------- >> >> ___________________________________________________________ >> 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/ -- ------------------------------------------- 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 -------------------------------------------