From danielfortin86@gmail.com Fri Oct 7 14:43:57 2016 From: D K To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo test with Date: Fri, 07 Oct 2016 11:43:55 -0700 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============5507566388841960588==" --===============5507566388841960588== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Thanks Nicola, That fixed it when all of the files are in the tmp/ directory Is this file/directory structure required when doing this? When I try putting the relevant entries in "galaxy-test/tool_data_table_conf.xml.test" and "galaxy-test/tool_data_table_conf.xml.sample" and the "twobit.loc" in "galaxy-test/test-data" and "galaxy-test/tool-data" then I get the same error again. I'd like to be able to put the files here instead of in their own directory structure. Thanks! On Fri, Oct 7, 2016 at 10:04 AM, D K wrote: > 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: > >> >> >> > 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 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_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/ >> >> >> > --===============5507566388841960588== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+VGhhbmtzIE5pY29sYSw8ZGl2Pjxicj48L2Rpdj48ZGl2PlRoYXQgZml4 ZWQgaXQgd2hlbiBhbGwgb2YgdGhlIGZpbGVzIGFyZSBpbiB0aGUgdG1wLyBkaXJlY3Rvcnk8L2Rp dj48ZGl2Pjxicj48L2Rpdj48ZGl2PklzIHRoaXMgZmlsZS9kaXJlY3Rvcnkgc3RydWN0dXJlIHJl cXVpcmVkIHdoZW4gZG9pbmcgdGhpcz88L2Rpdj48ZGl2Pjxicj48L2Rpdj48ZGl2PldoZW4gSSB0 cnkgcHV0dGluZyB0aGUgcmVsZXZhbnQgZW50cmllcyBpbiAmcXVvdDtnYWxheHktdGVzdC90b29s X2RhdGFfdGFibGVfY29uZi54bWwudGVzdCZxdW90OyBhbmQgwqAmcXVvdDtnYWxheHktdGVzdC90 b29sX2RhdGFfdGFibGVfY29uZi54bWwuc2FtcGxlJnF1b3Q7IGFuZCB0aGUgJnF1b3Q7dHdvYml0 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