From nsoranzo@tiscali.it Fri Oct 7 14:04:34 2016 From: Nicola Soranzo To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo test with Date: Fri, 07 Oct 2016 19:04:31 +0100 Message-ID: <87505cca-5a27-02dc-31e3-6967b4364e7a@tiscali.it> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6627726840262032225==" --===============6627726840262032225== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi D K, I think that the problem may be that the table name is different in your=20 test.xml , tool_data_table_conf.xml.sample and=20 tool_data_table_conf.xml.test files (type_indexes, twobit_indexes and=20 twobit respectively), should always be twobit. Cheers, Nicola On 07/10/16 18:04, D K wrote: > Hi Nicola, > > Thanks for the response, I'm still getting the same issue though. I've=20 > followed the set up you've shown for bowtie_wrappers but am getting=20 > 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: > > > > allow_duplicate_entries=3D"False"> > 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=20 > test.xml I've also tried putting these files under=20 > 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=20 > 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 refGenomeSourc= e_type requires a value, but has no legal values defined.\n >> >> From my script XML: >> >> > label=3D"Select a 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/reference_genomes/MFEprimer_index/Homo_sa= piens.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/ >> > --===============6627726840262032225== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+CiAgPGhlYWQ+CiAgICA8bWV0YSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9dXRm LTgiIGh0dHAtZXF1aXY9IkNvbnRlbnQtVHlwZSI+CiAgPC9oZWFkPgogIDxib2R5IGJnY29sb3I9 IiNGRkZGRkYiIHRleHQ9IiMwMDAwMDAiPgogICAgSGkgRCBLLDxicj4KICAgIEkgdGhpbmsgdGhh dCB0aGUgcHJvYmxlbSBtYXkgYmUgdGhhdCB0aGUgdGFibGUgbmFtZSBpcyBkaWZmZXJlbnQgaW4K ICAgIHlvdXIgdGVzdC54bWwgLCB0b29sX2RhdGFfdGFibGVfY29uZi54bWwuc2FtcGxlIGFuZAog ICAgdG9vbF9kYXRhX3RhYmxlX2NvbmYueG1sLnRlc3QgZmlsZXMgKHR5cGVfaW5kZXhlcywgdHdv Yml0X2luZGV4ZXMKICAgIGFuZCB0d29iaXQgcmVzcGVjdGl2ZWx5KSwgc2hvdWxkIGFsd2F5cyBi 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