From danielfortin86@gmail.com Fri Oct 7 13:04:44 2016 From: D K To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo test with Date: Fri, 07 Oct 2016 10:04:43 -0700 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============8316040706822219945==" --===============8316040706822219945== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Nicola, Thanks for the response, I'm still getting the same issue though. I've followed the set up you've shown for bowtie_wrappers but am getting the same error. I've changed my file structure to look like this: tmp/test.xml: > reference genome / transcriptome"> > > > > ... > > > > > tmp/tool_data_table_conf.xml.sample: > > > value, path > >
> tmp/tool_data_table_conf.xml.test: > > > > value, path > >
> tmp/tool-data/twobit.loc > hsapiens > /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.= fa tmp/tool-data/twobit.loc > # tmp/test-data/twobit.loc > hsapiens > /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.= fa Rather than placing these twobit.loc files etc... under tmp with test.xml I've also tried putting these files under galaxy-test/tool-data, test-data, etc... and that didn't help either. I'm not understanding what I'm doing wrong here. Any additional suggestions would be appreciated. Thanks! On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo wrote: > Hi D K, > for a good example of how to test parameters from data tables, please see: > https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_ > wrappers > > Your tool_data_table_conf.xml.test should be different from your .sample > and contain: > > > > Please note the use of ${__HERE__} to indicate the directory where the > tool is. > You should also have a comment-only tool-data/twobit.loc.sample , while > the loc file for testing should be in test-data/twobit.loc > > Cheers, > Nicola > > > On 06/10/16 23:08, 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_typ= e 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.te= st" > (mirrored) > >> > False"> >> value, name, path >> >>
> > > and from twobit.loc (where the columns are tab separated): > >> hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/ >> reference_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/ > > > --===============8316040706822219945== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+SGkgTmljb2xhLDxkaXY+PGJyPjwvZGl2PjxkaXY+VGhhbmtzIGZvciB0 aGUgcmVzcG9uc2UsIEkmIzM5O20gc3RpbGwgZ2V0dGluZyB0aGUgc2FtZSBpc3N1ZSB0aG91Z2gu IEkmIzM5O3ZlIGZvbGxvd2VkIHRoZSBzZXQgdXAgeW91JiMzOTt2ZSBzaG93biBmb3IgYm93dGll X3dyYXBwZXJzIGJ1dCBhbSBnZXR0aW5nIHRoZSBzYW1lIGVycm9yLjwvZGl2PjxkaXY+SSYjMzk7 dmUgY2hhbmdlZCBteSBmaWxlIHN0cnVjdHVyZSB0byBsb29rIGxpa2UgdGhpczo8L2Rpdj48ZGl2 Pjxicj48L2Rpdj48ZGl2PnRtcC90ZXN0LnhtbDo8L2Rpdj48ZGl2PjxibG9ja3F1b3RlIGNsYXNz PSJnbWFpbF9xdW90ZSIgc3R5bGU9Im1hcmdpbjowcHggMHB4IDBweCAwLjhleDtib3JkZXItbGVm 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