From p.j.a.cock@googlemail.com Fri Oct 7 05:06:28 2016 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo test with Date: Fri, 07 Oct 2016 10:06:26 +0100 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============1471500595092252892==" --===============1471500595092252892== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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_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/ > --===============1471500595092252892== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+SGkgREssPGRpdj48YnI+PC9kaXY+PGRpdj5Mb29raW5nIGF0IHlvdXIg WE1MIHRoYXQgbG9va3MgT0suPC9kaXY+PGRpdj48YnI+PGRpdj5JdCBtaWdodCBub3QgYmUgaW1w b3J0YW50LCBidXQgaG93IGV4YWN0bHkgYXJlIHlvdSBydW5uaW5nIHBsYW5lbW88L2Rpdj48ZGl2 PnRlc3Q/PC9kaXY+PGRpdj48ZGl2Pjxicj48L2Rpdj48ZGl2PkkmIzM5O20gYXNraW5nIGJlY2F1 c2UgY3VycmVudGx5IGl0IHdpbGwgbm90IGNyZWF0ZcKgPHNwYW4gc3R5bGU9ImZvbnQtc2l6ZTox Mi44cHgiPnRvb2wtZGF0YS90d29iaXQubG9jPC9zcGFuPjxicj48L2Rpdj48ZGl2PjxzcGFuIHN0 eWxlPSJmb250LXNpemU6MTIuOHB4Ij5mb3IgeW91IGZyb20geW91csKgPC9zcGFuPjxzcGFuIHN0 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