From danielfortin86@gmail.com Fri Oct 7 12:49:56 2016 From: D K To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo test with Date: Fri, 07 Oct 2016 09:49:55 -0700 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6746083727151162499==" --===============6746083727151162499== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Peter, This is the command I'm using to run planemo: . galaxy_test/.venv/bin/activate planemo test --test_data /home/galaxy-functional-testdata --galaxy_root galaxy-test/ --skip_venv test.xml I'm getting no errors when using the planemo lint tool. Thanks! On Fri, Oct 7, 2016 at 2:06 AM, Peter Cock wrote: > Hi DK, > > Looking at your XML that looks OK. > > It might not be important, but how exactly are you running planemo > test? > > I'm asking because currently it will not create tool-data/twobit.loc > for you from your sample file - although in that case I would have > expected a different error message: > > https://github.com/galaxyproject/planemo/issues/530 > https://github.com/galaxyproject/planemo/issues/530 > > Is planemo lint happy with your tool? > > Peter > > > On Thu, Oct 6, 2016 at 11:08 PM, D K wrote: > >> Hi galaxy-dev, >> >> I'm having a problem running a test using planemo where I would like the >> value of a parameter taken from one of the data tables. I get the following >> error in planemo: >> >> 'Error creating a job for these tool inputs - Parameter refGenomeSource_ty= pe requires a value, but has no legal values defined.\n >> >> >> From my script XML: >> >>> >> reference genome / transcriptome"> >>> >>> >>> >>> ... >>> >>> >>> >>> >>> >>> >>> From my "tool_data_table_conf.xml.sample" and >> "tool_data_table_conf.xml.test" (mirrored) >> >>> >> allow_duplicate_entries=3D"False"> >>> value, name, path >>> >>>
>> >> >> and from twobit.loc (where the columns are tab separated): >> >>> hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/refer >>> ence_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa >> >> >> Any suggestions would be greatly appreciated! >> >> >> ___________________________________________________________ >> 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/mailinglists/ >> > > --===============6746083727151162499== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+PHNwYW4gc3R5bGU9ImZvbnQtc2l6ZToxMi44cHgiPkhpIFBldGVyLDwv c3Bhbj48ZGl2IHN0eWxlPSJmb250LXNpemU6MTIuOHB4Ij48YnI+PC9kaXY+PGRpdiBzdHlsZT0i Zm9udC1zaXplOjEyLjhweCI+VGhpcyBpcyB0aGUgY29tbWFuZCBJJiMzOTttIHVzaW5nIHRvIHJ1 biBwbGFuZW1vOjwvZGl2PjxkaXYgc3R5bGU9ImZvbnQtc2l6ZToxMi44cHgiPi4gZ2FsYXh5X3Rl c3QvLnZlbnYvYmluL2FjdGl2YXRlPC9kaXY+PGRpdiBzdHlsZT0iZm9udC1zaXplOjEyLjhweCI+ cGxhbmVtbyB0ZXN0IC0tdGVzdF9kYXRhIC9ob21lL2dhbGF4eS1mdW5jdGlvbmFsLTx3YnI+dGVz dGRhdGEgLS1nYWxheHlfcm9vdCBnYWxheHktdGVzdC8gLS1za2lwX3ZlbnYgdGVzdC54bWw8YnI+ 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