From danielfortin86@gmail.com Thu Oct 6 18:08:57 2016 From: D K To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] planemo test with Date: Thu, 06 Oct 2016 15:08:55 -0700 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3621042626774055526==" --===============3621042626774055526== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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_type 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/reference_genomes/MFEprimer_index/Homo_sapiens.GRC= h38.cdna.all.fa Any suggestions would be greatly appreciated! --===============3621042626774055526== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+SGkgZ2FsYXh5LWRldiw8ZGl2Pjxicj48L2Rpdj48ZGl2PkkmIzM5O20g aGF2aW5nIGEgcHJvYmxlbSBydW5uaW5nIGEgdGVzdCB1c2luZyBwbGFuZW1vIHdoZXJlIEkgd291 bGQgbGlrZSB0aGUgdmFsdWUgb2YgYSBwYXJhbWV0ZXIgdGFrZW4gZnJvbSBvbmUgb2YgdGhlIGRh dGEgdGFibGVzLiBJIGdldCB0aGUgZm9sbG93aW5nIGVycm9yIGluIHBsYW5lbW86PC9kaXY+PGRp dj48ZGl2PjxwcmUgY2xhc3M9ImdtYWlsLXByZS1zY3JvbGxhYmxlIiBzdHlsZT0iYm94LXNpemlu Zzpib3JkZXItYm94O292ZXJmbG93LXg6YXV0bztvdmVyZmxvdy15OnNjcm9sbDtmb250LWZhbWls eTptZW5sbyxtb25hY28sY29uc29sYXMsJnF1b3Q7Y291cmllciBuZXcmcXVvdDssbW9ub3NwYWNl O2ZvbnQtc2l6ZToxM3B4O3BhZGRpbmc6OS41cHg7bWFyZ2luLXRvcDowcHg7bWFyZ2luLWJvdHRv bToxMHB4O21hcmdpbi1sZWZ0OjEwcHg7bGluZS1oZWlnaHQ6MS40Mjg1Nztjb2xvcjpyZ2IoNTEs NTEsNTEpO3dvcmQtYnJlYWs6YnJlYWstYWxsO3dvcmQtd3JhcDpicmVhay13b3JkO2JvcmRlcjox cHggc29saWQgcmdiKDIwNCwyMDQsMjA0KTtib3JkZXItcmFkaXVzOjRweDttYXgtaGVpZ2h0OjM0 MHB4O2JhY2tncm91bmQtY29sb3I6cmdiKDI0NSwyNDUsMjQ1KSI+JiMzOTtFcnJvciBjcmVhdGlu ZyBhIGpvYiBmb3IgdGhlc2UgdG9vbCBpbnB1dHMgLSBQYXJhbWV0ZXIgcmVmR2Vub21lU291cmNl X3R5cGUgcmVxdWlyZXMgYSB2YWx1ZSwgYnV0IGhhcyBubyBsZWdhbCB2YWx1ZXMgZGVmaW5lZC5c bjwvcHJlPjwvZGl2PjwvZGl2PjxkaXY+PGJyPjwvZGl2PjxkaXY+RnJvbSBteSBzY3JpcHQgWE1M OjwvZGl2PjxkaXY+PGJsb2NrcXVvdGUgY2xhc3M9ImdtYWlsX3F1b3RlIiBzdHlsZT0ibWFyZ2lu OjBweCAwcHggMHB4IDAuOGV4O2JvcmRlci1sZWZ0OjFweCBzb2xpZCByZ2IoMjA0LDIwNCwyMDQp O3BhZGRpbmctbGVmdDoxZXgiPsKgJmx0O3BhcmFtIG5hbWU9JnF1b3Q7cmVmR2Vub21lU291cmNl X3R5cGUmcXVvdDsgdHlwZT0mcXVvdDtzZWxlY3QmcXVvdDsgbGFiZWw9JnF1b3Q7U2VsZWN0IGEg cmVmZXJlbmNlIGdlbm9tZSAvIHRyYW5zY3JpcHRvbWUmcXVvdDsmZ3Q7PGJyPsKgIMKgIMKgICZs dDtvcHRpb25zIGZyb21fZGF0YV90YWJsZT0mcXVvdDt0eXBlX2luZGV4ZXMmcXVvdDsmZ3Q7PGJy PsKgIMKgIMKgICZsdDsvb3B0aW9ucyZndDs8YnI+Jmx0Oy9wYXJhbSZndDs8YnI+Li4uPGJyPsKg ICZsdDt0ZXN0cyZndDs8YnI+wqAgwqAgwqAgJmx0O3Rlc3QmZ3Q7PGJyPsKgIMKgIMKgIMKgICZs dDtwYXJhbSBuYW1lPSZxdW90O3JlZkdlbm9tZVNvdXJjZV90eXBlJnF1b3Q7IHZhbHVlPSZxdW90 O2hzYXBpZW5zJnF1b3Q7LyZndDs8YnI+wqAgwqAgwqAmbHQ7L3Rlc3QmZ3Q7PGJyPsKgICZsdDsv dGVzdHMmZ3Q7PGJyPjxicj48L2Jsb2NrcXVvdGU+PC9kaXY+PGRpdj5Gcm9tIG15ICZxdW90O3Rv b2xfZGF0YV90YWJsZV9jb25mLnhtbC5zYW1wbGUmcXVvdDsgYW5kICZxdW90O3Rvb2xfZGF0YV90 YWJsZV9jb25mLnhtbC50ZXN0JnF1b3Q7IChtaXJyb3JlZCk8L2Rpdj48YmxvY2txdW90ZSBjbGFz cz0iZ21haWxfcXVvdGUiIHN0eWxlPSJtYXJnaW46MHB4IDBweCAwcHggMC44ZXg7Ym9yZGVyLWxl ZnQ6MXB4IHNvbGlkIHJnYigyMDQsMjA0LDIwNCk7cGFkZGluZy1sZWZ0OjFleCI+Jmx0O3RhYmxl IG5hbWU9JnF1b3Q7dHlwZV9pbmRleGVzJnF1b3Q7IGNvbW1lbnRfY2hhcj0mcXVvdDsjJnF1b3Q7 IGFsbG93X2R1cGxpY2F0ZV9lbnRyaWVzPSZxdW90O0ZhbHNlJnF1b3Q7Jmd0Ozxicj7CoCDCoCDC oCDCoCAmbHQ7Y29sdW1ucyZndDt2YWx1ZSwgbmFtZSwgcGF0aCZsdDsvY29sdW1ucyZndDs8YnI+ wqAgwqAgwqAgwqAgJmx0O2ZpbGUgcGF0aD0mcXVvdDt0b29sLWRhdGEvdHdvYml0LmxvYyZxdW90 OyAvJmd0OyDCoCDCoDxicj4mbHQ7L3RhYmxlJmd0OzwvYmxvY2txdW90ZT48ZGl2Pjxicj48L2Rp dj48ZGl2PmFuZCBmcm9tIHR3b2JpdC5sb2MgKHdoZXJlIHRoZSBjb2x1bW5zIGFyZSB0YWIgc2Vw YXJhdGVkKTo8L2Rpdj48ZGl2PjxibG9ja3F1b3RlIGNsYXNzPSJnbWFpbF9xdW90ZSIgc3R5bGU9 Im1hcmdpbjowcHggMHB4IDBweCAwLjhleDtib3JkZXItbGVmdDoxcHggc29saWQgcmdiKDIwNCwy MDQsMjA0KTtwYWRkaW5nLWxlZnQ6MWV4Ij5oc2FwaWVucyDCoCDCoCDCoCDCoEguIHNhcGllbnMg KGhnMzgpIMKgIMKgIMKgIC9yZW1vdGUvUk1TL3VzZXJzL2dhbGF4eS9yZWZlcmVuY2VfZ2Vub21l cy9NRkVwcmltZXJfaW5kZXgvSG9tb19zYXBpZW5zLkdSQ2gzOC5jZG5hLmFsbC5mYTwvYmxvY2tx dW90ZT48ZGl2Pjxicj48L2Rpdj48ZGl2PkFueSBzdWdnZXN0aW9ucyB3b3VsZCBiZSBncmVhdGx5 IGFwcHJlY2lhdGVkIcKgPC9kaXY+PC9kaXY+PGRpdj48YnI+PC9kaXY+PC9kaXY+Cg== --===============3621042626774055526==-- 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="===============3168219386466779433==" --===============3168219386466779433== 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/ > --===============3168219386466779433== 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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galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] planemo test with Date: Fri, 07 Oct 2016 11:26:11 +0100 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============9106459307059717244==" --===============9106459307059717244== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi D K, for a good example of how to test parameters from data tables, please=20 see:=20 https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrapp= ers Your tool_data_table_conf.xml.test should be different from your .sample=20 and contain: Please note the use of ${__HERE__} to indicate the directory where the=20 tool is. You should also have a comment-only tool-data/twobit.loc.sample , while=20 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=20 > the value of a parameter taken from one of the data tables. I get the=20 > 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=20 > "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_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/ --===============9106459307059717244== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+CiAgPGhlYWQ+CiAgICA8bWV0YSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9dXRm LTgiIGh0dHAtZXF1aXY9IkNvbnRlbnQtVHlwZSI+CiAgPC9oZWFkPgogIDxib2R5IGJnY29sb3I9 IiNGRkZGRkYiIHRleHQ9IiMwMDAwMDAiPgogICAgSGkgRCBLLDxicj4KICAgIGZvciBhIGdvb2Qg ZXhhbXBsZSBvZiBob3cgdG8gdGVzdCBwYXJhbWV0ZXJzIGZyb20gZGF0YSB0YWJsZXMsCiAgICBw bGVhc2Ugc2VlOgo8YSBjbGFzcz0ibW96LXR4dC1saW5rLWZyZWV0ZXh0IiBocmVmPSJodHRwczov L2dpdGh1Yi5jb20vZ2FsYXh5cHJvamVjdC90b29scy1kZXZ0ZWFtL3RyZWUvbWFzdGVyL3Rvb2xz L2Jvd3RpZV93cmFwcGVycyI+aHR0cHM6Ly9naXRodWIuY29tL2dhbGF4eXByb2plY3QvdG9vbHMt 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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="===============6059329512189847649==" --===============6059329512189847649== 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/ >> > > --===============6059329512189847649== 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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PgpUbyBzZWFyY2ggR2FsYXh5IG1haWxpbmcgbGlzdHMgdXNlIHRoZSB1bmlmaWVkIHNlYXJjaCBh dDo8YnI+CsKgIDxhIGhyZWY9Imh0dHA6Ly9nYWxheHlwcm9qZWN0Lm9yZy9zZWFyY2gvbWFpbGlu Z2xpc3RzLyIgcmVsPSJub3JlZmVycmVyIiB0YXJnZXQ9Il9ibGFuayI+aHR0cDovL2dhbGF4eXBy b2plY3Qub3JnL3NlYXJjPHdicj5oL21haWxpbmdsaXN0cy88L2E+PGJyPjwvYmxvY2txdW90ZT48 L2Rpdj48YnI+PC9kaXY+CjwvYmxvY2txdW90ZT48L2Rpdj48YnI+PC9kaXY+Cg== --===============6059329512189847649==-- 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="===============7134747579337337113==" --===============7134747579337337113== 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/ > > > --===============7134747579337337113== 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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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="===============7119511223984030663==" --===============7119511223984030663== 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/ >> > --===============7119511223984030663== 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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aHR0cDovL2dhbGF4eXByb2plY3Qub3JnLzx3YnI+c2VhcmNoL21haWxpbmdsaXN0cy88L2E+PC9w cmU+CiAgICA8L3NwYW4+PC9ibG9ja3F1b3RlPgogICAgCgogIDwvZGl2PgoKPC9ibG9ja3F1b3Rl PjwvZGl2Pgo8L2Rpdj4KCgoKPC9ibG9ja3F1b3RlPgo8L2JvZHk+PC9odG1sPg== --===============7119511223984030663==-- 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="===============0997208142851515349==" --===============0997208142851515349== 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/ >> >> >> > --===============0997208142851515349== 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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